PDB Short entry for 2VI6 HEADER TRANSCRIPTION 28-NOV-07 2VI6 TITLE CRYSTAL STRUCTURE OF THE NANOG HOMEODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMEOBOX PROTEIN NANOG; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 FRAGMENT: HOMEODOMAIN, RESIDUES 96-155; COMPND 5 SYNONYM: HOMEOBOX TRANSCRIPTION FACTOR NANOG, EARLY EMBRYO SPECIFIC COMPND 6 EXPRESSION NK-TYPE HOMEOBOX PROTEIN, ES CELL- ASSOCIATED PROTEIN COMPND 7 4, NANOG; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETG60A KEYWDS HOMEODOMAIN, DNA-BINDING, TRANSCRIPTION, TRANSCRIPTION FACTOR, KEYWDS 2 DEVELOPMENTAL PROTEIN, TRANSCRIPTION REGULATION, NANOG, NUCLEUS, KEYWDS 3 HOMEOBOX, ACTIVATOR, REPRESSOR EXPDTA X-RAY DIFFRACTION AUTHOR R.JAUCH,C.K.L.NG,K.S.SAITAKENDU,R.C.STEVENS,P.R.KOLATKAR REVDAT 4 13-JUL-11 2VI6 1 VERSN REVDAT 3 24-FEB-09 2VI6 1 VERSN REVDAT 2 19-FEB-08 2VI6 1 JRNL REVDAT 1 15-JAN-08 2VI6 0 JRNL AUTH R.JAUCH,C.K.L.NG,K.S.SAITAKENDU,R.C.STEVENS,P.R.KOLATKAR JRNL TITL CRYSTAL STRUCTURE AND DNA BINDING OF THE HOMEODOMAIN OF THE JRNL TITL 2 STEM CELL TRANSCRIPTION FACTOR NANOG. JRNL REF J.MOL.BIOL. V. 376 758 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18177668 JRNL DOI 10.1016/J.JMB.2007.11.091 REMARK 2 REMARK 2 RESOLUTION. 2.6 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 19601 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1040 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1094 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3600 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.3980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3763 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 69 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.24000 REMARK 3 B22 (A**2) : -2.70000 REMARK 3 B33 (A**2) : 4.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.23000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.571 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.320 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.242 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 23.396 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3831 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5106 ; 1.193 ; 1.930 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 429 ; 4.777 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 200 ;39.908 ;24.800 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 829 ;19.611 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;13.873 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 530 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2772 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1560 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2605 ; 0.298 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 108 ; 0.140 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 55 ; 0.399 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.188 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2250 ; 0.485 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3493 ; 0.878 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1846 ; 1.231 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1613 ; 1.971 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 60 REMARK 3 ORIGIN FOR THE GROUP (A): 20.8972 36.8960 43.0032 REMARK 3 T TENSOR REMARK 3 T11: -0.0612 T22: -0.1902 REMARK 3 T33: -0.0776 T12: -0.0018 REMARK 3 T13: 0.0373 T23: -0.0360 REMARK 3 L TENSOR REMARK 3 L11: 2.7097 L22: 11.1122 REMARK 3 L33: 5.7943 L12: 1.8204 REMARK 3 L13: 0.0145 L23: -3.4616 REMARK 3 S TENSOR REMARK 3 S11: 0.0219 S12: 0.0039 S13: 0.1990 REMARK 3 S21: -0.0098 S22: -0.0098 S23: 0.0370 REMARK 3 S31: -0.1967 S32: 0.1410 S33: -0.0121 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 7 B 60 REMARK 3 ORIGIN FOR THE GROUP (A): 46.1109 61.6297 41.5968 REMARK 3 T TENSOR REMARK 3 T11: -0.1019 T22: -0.0489 REMARK 3 T33: -0.0243 T12: -0.0342 REMARK 3 T13: -0.0591 T23: -0.0410 REMARK 3 L TENSOR REMARK 3 L11: 16.8481 L22: 1.2269 REMARK 3 L33: 2.1403 L12: 2.3935 REMARK 3 L13: 0.4260 L23: -0.9347 REMARK 3 S TENSOR REMARK 3 S11: 0.0232 S12: -0.6510 S13: 0.0123 REMARK 3 S21: 0.1054 S22: -0.0785 S23: 0.0162 REMARK 3 S31: -0.0862 S32: 0.1328 S33: 0.0553 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 6 C 60 REMARK 3 ORIGIN FOR THE GROUP (A): 25.2893 67.8159 39.8445 REMARK 3 T TENSOR REMARK 3 T11: -0.0881 T22: -0.1423 REMARK 3 T33: -0.0757 T12: -0.0027 REMARK 3 T13: 0.0801 T23: 0.0304 REMARK 3 L TENSOR REMARK 3 L11: 7.4803 L22: 16.1526 REMARK 3 L33: 1.1416 L12: -3.1264 REMARK 3 L13: 0.6165 L23: -0.1741 REMARK 3 S TENSOR REMARK 3 S11: -0.0581 S12: 0.1330 S13: 0.3514 REMARK 3 S21: 0.6901 S22: 0.2187 S23: -0.2114 REMARK 3 S31: -0.0030 S32: -0.0404 S33: -0.1606 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 6 D 60 REMARK 3 ORIGIN FOR THE GROUP (A): 12.1411 59.4313 69.2244 REMARK 3 T TENSOR REMARK 3 T11: -0.0909 T22: -0.1286 REMARK 3 T33: -0.0677 T12: -0.0288 REMARK 3 T13: -0.0801 T23: -0.0642 REMARK 3 L TENSOR REMARK 3 L11: 10.9850 L22: 6.1674 REMARK 3 L33: 11.5485 L12: -3.5856 REMARK 3 L13: 8.1421 L23: -2.3048 REMARK 3 S TENSOR REMARK 3 S11: 0.7361 S12: 0.3318 S13: -1.0742 REMARK 3 S21: -0.0879 S22: -0.1095 S23: 0.2243 REMARK 3 S31: 0.7363 S32: -0.1368 S33: -0.6266 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 7 E 60 REMARK 3 ORIGIN FOR THE GROUP (A): 23.4197 76.1597 75.8197 REMARK 3 T TENSOR REMARK 3 T11: -0.0744 T22: -0.1715 REMARK 3 T33: -0.1345 T12: 0.0223 REMARK 3 T13: -0.0271 T23: 0.0399 REMARK 3 L TENSOR REMARK 3 L11: 20.6970 L22: 9.2223 REMARK 3 L33: 6.7508 L12: -5.0016 REMARK 3 L13: 9.7548 L23: -1.8282 REMARK 3 S TENSOR REMARK 3 S11: -0.7273 S12: 0.5152 S13: 1.2150 REMARK 3 S21: 0.7847 S22: -0.0284 S23: -1.0327 REMARK 3 S31: -0.3179 S32: 0.1860 S33: 0.7557 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 6 F 60 REMARK 3 ORIGIN FOR THE GROUP (A): -0.8383 74.0908 56.1177 REMARK 3 T TENSOR REMARK 3 T11: -0.2606 T22: 0.1457 REMARK 3 T33: -0.2078 T12: 0.0501 REMARK 3 T13: 0.0027 T23: 0.0802 REMARK 3 L TENSOR REMARK 3 L11: 11.8658 L22: 6.9012 REMARK 3 L33: 11.0460 L12: 1.8270 REMARK 3 L13: 1.5010 L23: -0.8311 REMARK 3 S TENSOR REMARK 3 S11: 0.1503 S12: 1.0769 S13: 0.3064 REMARK 3 S21: -0.3025 S22: 0.0594 S23: 0.1477 REMARK 3 S31: -0.0357 S32: 0.1972 S33: -0.2096 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : G 6 G 60 REMARK 3 ORIGIN FOR THE GROUP (A): 11.7333 54.4171 30.4267 REMARK 3 T TENSOR REMARK 3 T11: -0.1135 T22: -0.1005 REMARK 3 T33: 0.0591 T12: -0.1086 REMARK 3 T13: -0.0666 T23: 0.1098 REMARK 3 L TENSOR REMARK 3 L11: 5.6802 L22: 19.3998 REMARK 3 L33: 5.3190 L12: -0.5774 REMARK 3 L13: 1.1003 L23: -4.5101 REMARK 3 S TENSOR REMARK 3 S11: -0.1549 S12: 0.3443 S13: 0.2525 REMARK 3 S21: -0.9166 S22: 0.3567 S23: 0.7889 REMARK 3 S31: 0.0611 S32: -0.2538 S33: -0.2018 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 7 H 60 REMARK 3 ORIGIN FOR THE GROUP (A): 11.2016 85.1688 34.3696 REMARK 3 T TENSOR REMARK 3 T11: -0.0599 T22: -0.1516 REMARK 3 T33: 0.0018 T12: 0.1122 REMARK 3 T13: 0.1353 T23: 0.2539 REMARK 3 L TENSOR REMARK 3 L11: 12.2837 L22: 6.3878 REMARK 3 L33: 7.5515 L12: 0.6870 REMARK 3 L13: -5.2643 L23: -0.2949 REMARK 3 S TENSOR REMARK 3 S11: 0.2392 S12: -0.1857 S13: 0.1050 REMARK 3 S21: 0.2110 S22: 0.1702 S23: 0.6561 REMARK 3 S31: -0.3055 S32: -0.5742 S33: -0.4095 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. FIRST 7 N-TERMINAL RESIDUES DISORDERED REMARK 4 REMARK 4 2VI6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-NOV-07. REMARK 100 THE PDBE ID CODE IS EBI-34590. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20786 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.60 REMARK 200 RESOLUTION RANGE LOW (A) : 50.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 3.7 REMARK 200 R MERGE (I) : 0.07 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.40 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.2 REMARK 200 R MERGE FOR SHELL (I) : 0.52 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.40 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1IG7 REMARK 200 REMARK 200 REMARK: DNA REMOVED FROM STARTING MODEL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.2 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 52.65900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.38550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.65900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 57.38550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 5 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: E REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 6 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: F REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 7 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: G REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 8 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: H REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 THR A 0 REMARK 465 LYS A 1 REMARK 465 GLN A 2 REMARK 465 LYS A 3 REMARK 465 MET A 4 REMARK 465 ARG A 5 REMARK 465 GLY B -1 REMARK 465 THR B 0 REMARK 465 LYS B 1 REMARK 465 GLN B 2 REMARK 465 LYS B 3 REMARK 465 MET B 4 REMARK 465 ARG B 5 REMARK 465 THR B 6 REMARK 465 GLY C -1 REMARK 465 THR C 0 REMARK 465 LYS C 1 REMARK 465 GLN C 2 REMARK 465 LYS C 3 REMARK 465 MET C 4 REMARK 465 ARG C 5 REMARK 465 GLY D -1 REMARK 465 THR D 0 REMARK 465 LYS D 1 REMARK 465 GLN D 2 REMARK 465 LYS D 3 REMARK 465 MET D 4 REMARK 465 ARG D 5 REMARK 465 GLY E -1 REMARK 465 THR E 0 REMARK 465 LYS E 1 REMARK 465 GLN E 2 REMARK 465 LYS E 3 REMARK 465 MET E 4 REMARK 465 ARG E 5 REMARK 465 THR E 6 REMARK 465 GLY F -1 REMARK 465 THR F 0 REMARK 465 LYS F 1 REMARK 465 GLN F 2 REMARK 465 LYS F 3 REMARK 465 MET F 4 REMARK 465 ARG F 5 REMARK 465 GLY G -1 REMARK 465 THR G 0 REMARK 465 LYS G 1 REMARK 465 GLN G 2 REMARK 465 LYS G 3 REMARK 465 MET G 4 REMARK 465 ARG G 5 REMARK 465 GLY H -1 REMARK 465 THR H 0 REMARK 465 LYS H 1 REMARK 465 GLN H 2 REMARK 465 LYS H 3 REMARK 465 MET H 4 REMARK 465 ARG H 5 REMARK 465 THR H 6 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS E 43 CD LYS E 43 CE 0.245 REMARK 500 LYS E 43 CE LYS E 43 NZ 0.209 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS E 43 CD - CE - NZ ANGL. DEV. = -17.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL D 7 9.52 -150.82 REMARK 500 GLN D 23 118.99 -160.14 REMARK 500 GLN E 23 115.32 -173.57 REMARK 500 SER E 27 -163.82 -65.56 REMARK 500 LYS G 57 -70.04 0.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 CYS G 56 LYS G 57 145.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 GT DIPEPTIDE DERVIED FROM THE EXPRESSION VECTOR DBREF 2VI6 A -1 0 PDB 2VI6 2VI6 -1 0 DBREF 2VI6 A 1 60 UNP Q80Z64 NANOG_MOUSE 96 155 DBREF 2VI6 B -1 0 PDB 2VI6 2VI6 -1 0 DBREF 2VI6 B 1 60 UNP Q80Z64 NANOG_MOUSE 96 155 DBREF 2VI6 C -1 0 PDB 2VI6 2VI6 -1 0 DBREF 2VI6 C 1 60 UNP Q80Z64 NANOG_MOUSE 96 155 DBREF 2VI6 D -1 0 PDB 2VI6 2VI6 -1 0 DBREF 2VI6 D 1 60 UNP Q80Z64 NANOG_MOUSE 96 155 DBREF 2VI6 E -1 0 PDB 2VI6 2VI6 -1 0 DBREF 2VI6 E 1 60 UNP Q80Z64 NANOG_MOUSE 96 155 DBREF 2VI6 F -1 0 PDB 2VI6 2VI6 -1 0 DBREF 2VI6 F 1 60 UNP Q80Z64 NANOG_MOUSE 96 155 DBREF 2VI6 G -1 0 PDB 2VI6 2VI6 -1 0 DBREF 2VI6 G 1 60 UNP Q80Z64 NANOG_MOUSE 96 155 DBREF 2VI6 H -1 0 PDB 2VI6 2VI6 -1 0 DBREF 2VI6 H 1 60 UNP Q80Z64 NANOG_MOUSE 96 155 SEQRES 1 A 62 GLY THR LYS GLN LYS MET ARG THR VAL PHE SER GLN ALA SEQRES 2 A 62 GLN LEU CYS ALA LEU LYS ASP ARG PHE GLN LYS GLN LYS SEQRES 3 A 62 TYR LEU SER LEU GLN GLN MET GLN GLU LEU SER SER ILE SEQRES 4 A 62 LEU ASN LEU SER TYR LYS GLN VAL LYS THR TRP PHE GLN SEQRES 5 A 62 ASN GLN ARG MET LYS CYS LYS ARG TRP GLN SEQRES 1 B 62 GLY THR LYS GLN LYS MET ARG THR VAL PHE SER GLN ALA SEQRES 2 B 62 GLN LEU CYS ALA LEU LYS ASP ARG PHE GLN LYS GLN LYS SEQRES 3 B 62 TYR LEU SER LEU GLN GLN MET GLN GLU LEU SER SER ILE SEQRES 4 B 62 LEU ASN LEU SER TYR LYS GLN VAL LYS THR TRP PHE GLN SEQRES 5 B 62 ASN GLN ARG MET LYS CYS LYS ARG TRP GLN SEQRES 1 C 62 GLY THR LYS GLN LYS MET ARG THR VAL PHE SER GLN ALA SEQRES 2 C 62 GLN LEU CYS ALA LEU LYS ASP ARG PHE GLN LYS GLN LYS SEQRES 3 C 62 TYR LEU SER LEU GLN GLN MET GLN GLU LEU SER SER ILE SEQRES 4 C 62 LEU ASN LEU SER TYR LYS GLN VAL LYS THR TRP PHE GLN SEQRES 5 C 62 ASN GLN ARG MET LYS CYS LYS ARG TRP GLN SEQRES 1 D 62 GLY THR LYS GLN LYS MET ARG THR VAL PHE SER GLN ALA SEQRES 2 D 62 GLN LEU CYS ALA LEU LYS ASP ARG PHE GLN LYS GLN LYS SEQRES 3 D 62 TYR LEU SER LEU GLN GLN MET GLN GLU LEU SER SER ILE SEQRES 4 D 62 LEU ASN LEU SER TYR LYS GLN VAL LYS THR TRP PHE GLN SEQRES 5 D 62 ASN GLN ARG MET LYS CYS LYS ARG TRP GLN SEQRES 1 E 62 GLY THR LYS GLN LYS MET ARG THR VAL PHE SER GLN ALA SEQRES 2 E 62 GLN LEU CYS ALA LEU LYS ASP ARG PHE GLN LYS GLN LYS SEQRES 3 E 62 TYR LEU SER LEU GLN GLN MET GLN GLU LEU SER SER ILE SEQRES 4 E 62 LEU ASN LEU SER TYR LYS GLN VAL LYS THR TRP PHE GLN SEQRES 5 E 62 ASN GLN ARG MET LYS CYS LYS ARG TRP GLN SEQRES 1 F 62 GLY THR LYS GLN LYS MET ARG THR VAL PHE SER GLN ALA SEQRES 2 F 62 GLN LEU CYS ALA LEU LYS ASP ARG PHE GLN LYS GLN LYS SEQRES 3 F 62 TYR LEU SER LEU GLN GLN MET GLN GLU LEU SER SER ILE SEQRES 4 F 62 LEU ASN LEU SER TYR LYS GLN VAL LYS THR TRP PHE GLN SEQRES 5 F 62 ASN GLN ARG MET LYS CYS LYS ARG TRP GLN SEQRES 1 G 62 GLY THR LYS GLN LYS MET ARG THR VAL PHE SER GLN ALA SEQRES 2 G 62 GLN LEU CYS ALA LEU LYS ASP ARG PHE GLN LYS GLN LYS SEQRES 3 G 62 TYR LEU SER LEU GLN GLN MET GLN GLU LEU SER SER ILE SEQRES 4 G 62 LEU ASN LEU SER TYR LYS GLN VAL LYS THR TRP PHE GLN SEQRES 5 G 62 ASN GLN ARG MET LYS CYS LYS ARG TRP GLN SEQRES 1 H 62 GLY THR LYS GLN LYS MET ARG THR VAL PHE SER GLN ALA SEQRES 2 H 62 GLN LEU CYS ALA LEU LYS ASP ARG PHE GLN LYS GLN LYS SEQRES 3 H 62 TYR LEU SER LEU GLN GLN MET GLN GLU LEU SER SER ILE SEQRES 4 H 62 LEU ASN LEU SER TYR LYS GLN VAL LYS THR TRP PHE GLN SEQRES 5 H 62 ASN GLN ARG MET LYS CYS LYS ARG TRP GLN FORMUL 9 HOH *69(H2 O) HELIX 1 1 SER A 9 GLN A 23 1 15 HELIX 2 2 SER A 27 ASN A 39 1 13 HELIX 3 3 SER A 41 LYS A 55 1 15 HELIX 4 4 CYS A 56 GLN A 60 5 5 HELIX 5 5 SER B 9 GLN B 23 1 15 HELIX 6 6 SER B 27 ASN B 39 1 13 HELIX 7 7 SER B 41 MET B 54 1 14 HELIX 8 8 LYS B 55 GLN B 60 5 6 HELIX 9 9 SER C 9 GLN C 23 1 15 HELIX 10 10 SER C 27 ASN C 39 1 13 HELIX 11 11 SER C 41 MET C 54 1 14 HELIX 12 12 LYS C 55 GLN C 60 5 6 HELIX 13 13 SER D 9 GLN D 21 1 13 HELIX 14 14 SER D 27 ASN D 39 1 13 HELIX 15 15 SER D 41 CYS D 56 1 16 HELIX 16 16 LYS D 57 GLN D 60 5 4 HELIX 17 17 SER E 9 GLN E 21 1 13 HELIX 18 18 SER E 27 LEU E 38 1 12 HELIX 19 19 SER E 41 LYS E 55 1 15 HELIX 20 20 CYS E 56 GLN E 60 5 5 HELIX 21 21 SER F 9 GLN F 23 1 15 HELIX 22 22 SER F 27 ASN F 39 1 13 HELIX 23 23 SER F 41 LYS F 55 1 15 HELIX 24 24 CYS F 56 GLN F 60 5 5 HELIX 25 25 SER G 9 GLN G 23 1 15 HELIX 26 26 SER G 27 ASN G 39 1 13 HELIX 27 27 SER G 41 MET G 54 1 14 HELIX 28 28 LYS G 55 GLN G 60 5 6 HELIX 29 29 SER H 9 GLN H 21 1 13 HELIX 30 30 SER H 27 ASN H 39 1 13 HELIX 31 31 SER H 41 CYS H 56 1 16 HELIX 32 32 LYS H 57 GLN H 60 5 4 SSBOND 1 CYS C 14 CYS G 56 1555 1555 2.03 SSBOND 2 CYS C 56 CYS G 14 1555 1555 2.05 SSBOND 3 CYS D 14 CYS E 56 1555 1555 2.04 SSBOND 4 CYS D 56 CYS E 14 1555 1555 2.02 CRYST1 105.318 114.771 62.771 90.00 98.68 90.00 C 1 2 1 32 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009495 0.000000 0.001450 0.00000 SCALE2 0.000000 0.008713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016115 0.00000 MTRIX1 1 0.296178 -0.828859 -0.474628 77.89930 1 MTRIX2 1 0.831273 -0.021035 0.555467 -23.23910 1 MTRIX3 1 -0.470387 -0.559062 0.682778 70.59430 1 MTRIX1 2 -0.725684 -0.446251 0.523682 48.65920 1 MTRIX2 2 0.686929 -0.426914 0.588110 25.07290 1 MTRIX3 2 -0.038878 0.786515 0.616347 -33.87040 1 MTRIX1 3 0.850005 0.219070 -0.479061 30.68910 1 MTRIX2 3 0.362741 -0.902871 0.230743 70.12920 1 MTRIX3 3 -0.381982 -0.369908 -0.846911 128.11620 1 MTRIX1 4 0.036894 -0.324991 -0.944997 116.26940 1 MTRIX2 4 -0.321237 0.891594 -0.319167 0.81160 1 MTRIX3 4 0.946280 0.315343 -0.071504 2.14290 1 MTRIX1 5 -0.312064 0.790285 0.527319 -67.53470 1 MTRIX2 5 0.869375 0.013697 0.493963 8.90670 1 MTRIX3 5 0.383149 0.612587 -0.691328 36.70580 1 MTRIX1 6 -0.301956 0.494814 0.814851 -27.27450 1 MTRIX2 6 -0.737174 0.420785 -0.528692 38.72190 1 MTRIX3 6 -0.604481 -0.760328 0.237705 84.25030 1 MTRIX1 7 -0.320536 0.054304 -0.945679 52.25640 1 MTRIX2 7 -0.017064 -0.998524 -0.051555 123.90300 1 MTRIX3 7 -0.947083 -0.000388 0.320990 42.43740 1