PDB Short entry for 3DB5 HEADER TRANSFERASE 30-MAY-08 3DB5 TITLE CRYSTAL STRUCTURE OF METHYLTRANSFERASE DOMAIN OF HUMAN PR DOMAIN- TITLE 2 CONTAINING PROTEIN 4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PR DOMAIN ZINC FINGER PROTEIN 4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 390-540; COMPND 5 SYNONYM: PR DOMAIN-CONTAINING PROTEIN 4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: PRDM4, PFM1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS METHYLTRANSFERASE, PRDM4, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, SGC, DNA-BINDING, METAL-BINDING, NUCLEUS, TRANSCRIPTION, KEYWDS 3 TRANSCRIPTION REGULATION, ZINC-FINGER, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.F.AMAYA,H.ZENG,P.LOPPNAU,C.BOUNTRA,J.WEIGELT,C.H.ARROWSMITH, AUTHOR 2 A.M.EDWARDS,A.BOCHKAREV,J.MIN,A.N.PLOTNIKOV,H.WU,STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (SGC) REVDAT 4 25-OCT-17 3DB5 1 REMARK REVDAT 3 13-JUL-11 3DB5 1 VERSN REVDAT 2 24-FEB-09 3DB5 1 VERSN REVDAT 1 12-AUG-08 3DB5 0 JRNL AUTH H.ZENG,M.F.AMAYA,P.LOPPNAU,A.BOCHKAREV,J.MIN,A.N.PLOTNIKOV, JRNL AUTH 2 H.WU JRNL TITL THE CRYSTAL STRUCTURE OF METHYLTRANSFERASE DOMAIN OF HUMAN JRNL TITL 2 PR DOMAIN-CONTAINING PROTEIN 4. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 21490 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) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1101 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1449 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2062 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 139 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) : 24.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.27000 REMARK 3 B22 (A**2) : -0.27000 REMARK 3 B33 (A**2) : 0.55000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.212 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.214 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.143 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.423 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.867 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2117 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2882 ; 1.926 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 252 ;10.324 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;37.353 ;24.038 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 329 ;17.269 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;20.654 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 316 ; 0.150 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1633 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 822 ; 0.226 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1419 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 136 ; 0.170 ; 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): 67 ; 0.255 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.157 ; 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): 1326 ; 1.240 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2094 ; 2.007 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 915 ; 3.007 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 788 ; 4.499 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 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 4 A 77 REMARK 3 ORIGIN FOR THE GROUP (A): 29.7520 46.8490 21.5253 REMARK 3 T TENSOR REMARK 3 T11: 0.1008 T22: 0.0344 REMARK 3 T33: 0.1020 T12: -0.0116 REMARK 3 T13: 0.0579 T23: -0.0291 REMARK 3 L TENSOR REMARK 3 L11: 1.0206 L22: 3.4778 REMARK 3 L33: 2.2892 L12: 0.0991 REMARK 3 L13: -0.2426 L23: 2.7584 REMARK 3 S TENSOR REMARK 3 S11: -0.0777 S12: 0.0562 S13: -0.0679 REMARK 3 S21: 0.2027 S22: -0.0189 S23: 0.1249 REMARK 3 S31: -0.0629 S32: 0.0392 S33: 0.0966 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 : A 78 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): 27.5215 39.4688 11.5205 REMARK 3 T TENSOR REMARK 3 T11: 0.0963 T22: 0.0549 REMARK 3 T33: 0.1023 T12: 0.0093 REMARK 3 T13: 0.0527 T23: -0.1002 REMARK 3 L TENSOR REMARK 3 L11: 3.5445 L22: 2.0095 REMARK 3 L33: 2.5224 L12: -0.0547 REMARK 3 L13: 0.1102 L23: 0.3487 REMARK 3 S TENSOR REMARK 3 S11: -0.0319 S12: 0.3088 S13: -0.1486 REMARK 3 S21: -0.1251 S22: -0.0672 S23: 0.0884 REMARK 3 S31: 0.0105 S32: -0.1373 S33: 0.0991 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 : B 2 B 89 REMARK 3 ORIGIN FOR THE GROUP (A): 33.3687 3.1436 25.2345 REMARK 3 T TENSOR REMARK 3 T11: 0.1877 T22: 0.0168 REMARK 3 T33: 0.1686 T12: 0.0193 REMARK 3 T13: 0.1796 T23: 0.0349 REMARK 3 L TENSOR REMARK 3 L11: 0.7662 L22: 3.7268 REMARK 3 L33: 1.6231 L12: 1.6180 REMARK 3 L13: -1.0108 L23: -1.8349 REMARK 3 S TENSOR REMARK 3 S11: -0.1047 S12: -0.0342 S13: -0.2557 REMARK 3 S21: -0.3530 S22: -0.2759 S23: -0.3894 REMARK 3 S31: 0.2703 S32: 0.1385 S33: 0.3806 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 : B 90 B 148 REMARK 3 ORIGIN FOR THE GROUP (A): 33.7324 9.7897 15.4612 REMARK 3 T TENSOR REMARK 3 T11: 0.2138 T22: -0.0150 REMARK 3 T33: 0.0949 T12: 0.0223 REMARK 3 T13: 0.1847 T23: 0.0200 REMARK 3 L TENSOR REMARK 3 L11: 1.9700 L22: 3.9626 REMARK 3 L33: 3.8548 L12: 0.8262 REMARK 3 L13: -0.3913 L23: -0.8707 REMARK 3 S TENSOR REMARK 3 S11: -0.1818 S12: 0.0934 S13: -0.1328 REMARK 3 S21: -0.5997 S22: -0.1393 S23: -0.2527 REMARK 3 S31: 0.3959 S32: 0.0998 S33: 0.3211 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: NULL REMARK 4 REMARK 4 3DB5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000047818. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E DW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21499 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 27.20 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 18.20 REMARK 200 R MERGE FOR SHELL (I) : 0.79900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 MICROLITER PROTEIN SOLUTION, 1.5 REMARK 280 MICROLITER RESERVOIR SOLUTION CONTAINING 23% PEG 3350, 0.2 M REMARK 280 AMMONIUM ACETATE, 0.1 M BIS-TRIS PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 53.64700 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 53.64700 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 66.82100 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 53.64700 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 53.64700 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 66.82100 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 53.64700 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 53.64700 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 66.82100 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 53.64700 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 53.64700 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 66.82100 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 53.64700 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 53.64700 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 66.82100 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 53.64700 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 53.64700 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 66.82100 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 53.64700 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 53.64700 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 66.82100 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 53.64700 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 53.64700 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 66.82100 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS REMARK 300 EXPERIMENTALLY UNKNOWN. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 172 LIES ON A SPECIAL POSITION. 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 GLU A 1 REMARK 465 HIS A 2 REMARK 465 GLY A 3 REMARK 465 VAL A 32 REMARK 465 GLY A 33 REMARK 465 ALA A 34 REMARK 465 SER A 60 REMARK 465 MSE A 61 REMARK 465 GLU A 62 REMARK 465 VAL A 63 REMARK 465 ALA A 64 REMARK 465 GLU A 65 REMARK 465 TRP A 66 REMARK 465 THR A 67 REMARK 465 ASP A 68 REMARK 465 LYS A 69 REMARK 465 ALA A 70 REMARK 465 ASP A 142 REMARK 465 TYR A 143 REMARK 465 ALA A 144 REMARK 465 GLN A 145 REMARK 465 GLN A 146 REMARK 465 ILE A 147 REMARK 465 GLY A 148 REMARK 465 VAL A 149 REMARK 465 PRO A 150 REMARK 465 GLU A 151 REMARK 465 GLU B 1 REMARK 465 VAL B 32 REMARK 465 GLY B 33 REMARK 465 GLU B 62 REMARK 465 VAL B 63 REMARK 465 ALA B 64 REMARK 465 GLU B 65 REMARK 465 TRP B 66 REMARK 465 THR B 67 REMARK 465 ASP B 68 REMARK 465 LYS B 69 REMARK 465 ALA B 70 REMARK 465 VAL B 71 REMARK 465 ASN B 72 REMARK 465 VAL B 149 REMARK 465 PRO B 150 REMARK 465 GLU B 151 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ILE A 13 CG1 CG2 CD1 REMARK 470 LYS A 23 CG CD CE NZ REMARK 470 HIS A 59 CG ND1 CD2 CE1 NE2 REMARK 470 VAL A 71 CG1 CG2 REMARK 470 LYS A 120 CE NZ REMARK 470 ARG A 141 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 2 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 23 CD CE NZ REMARK 470 MSE B 61 CG SE CE REMARK 470 LYS B 76 CE NZ REMARK 470 ARG B 105 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 106 CG OD1 ND2 REMARK 470 ARG B 141 CD NE CZ NH1 NH2 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 GLU A 109 CB GLU A 109 CG -0.143 REMARK 500 HIS B 2 C HIS B 2 O 0.119 REMARK 500 ILE B 31 C ILE B 31 O 0.182 REMARK 500 GLU B 109 CB GLU B 109 CG -0.117 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 ARG B 107 N - CA - C ANGL. DEV. = -26.4 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 A 46 154.16 -44.18 REMARK 500 ASN A 72 -10.92 75.93 REMARK 500 ARG B 47 49.86 -102.86 REMARK 500 ASN B 106 167.98 175.35 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 ASN B 106 ARG B 107 -116.23 REMARK 500 REMARK 500 REMARK: NULL DBREF 3DB5 A 1 151 UNP Q9UKN5 PRDM4_HUMAN 390 540 DBREF 3DB5 B 1 151 UNP Q9UKN5 PRDM4_HUMAN 390 540 SEQRES 1 A 151 GLU HIS GLY PRO VAL THR PHE VAL PRO ASP THR PRO ILE SEQRES 2 A 151 GLU SER ARG ALA ARG LEU SER LEU PRO LYS GLN LEU VAL SEQRES 3 A 151 LEU ARG GLN SER ILE VAL GLY ALA GLU VAL GLY VAL TRP SEQRES 4 A 151 THR GLY GLU THR ILE PRO VAL ARG THR CYS PHE GLY PRO SEQRES 5 A 151 LEU ILE GLY GLN GLN SER HIS SER MSE GLU VAL ALA GLU SEQRES 6 A 151 TRP THR ASP LYS ALA VAL ASN HIS ILE TRP LYS ILE TYR SEQRES 7 A 151 HIS ASN GLY VAL LEU GLU PHE CYS ILE ILE THR THR ASP SEQRES 8 A 151 GLU ASN GLU CYS ASN TRP MSE MSE PHE VAL ARG LYS ALA SEQRES 9 A 151 ARG ASN ARG GLU GLU GLN ASN LEU VAL ALA TYR PRO HIS SEQRES 10 A 151 ASP GLY LYS ILE PHE PHE CYS THR SER GLN ASP ILE PRO SEQRES 11 A 151 PRO GLU ASN GLU LEU LEU PHE TYR TYR SER ARG ASP TYR SEQRES 12 A 151 ALA GLN GLN ILE GLY VAL PRO GLU SEQRES 1 B 151 GLU HIS GLY PRO VAL THR PHE VAL PRO ASP THR PRO ILE SEQRES 2 B 151 GLU SER ARG ALA ARG LEU SER LEU PRO LYS GLN LEU VAL SEQRES 3 B 151 LEU ARG GLN SER ILE VAL GLY ALA GLU VAL GLY VAL TRP SEQRES 4 B 151 THR GLY GLU THR ILE PRO VAL ARG THR CYS PHE GLY PRO SEQRES 5 B 151 LEU ILE GLY GLN GLN SER HIS SER MSE GLU VAL ALA GLU SEQRES 6 B 151 TRP THR ASP LYS ALA VAL ASN HIS ILE TRP LYS ILE TYR SEQRES 7 B 151 HIS ASN GLY VAL LEU GLU PHE CYS ILE ILE THR THR ASP SEQRES 8 B 151 GLU ASN GLU CYS ASN TRP MSE MSE PHE VAL ARG LYS ALA SEQRES 9 B 151 ARG ASN ARG GLU GLU GLN ASN LEU VAL ALA TYR PRO HIS SEQRES 10 B 151 ASP GLY LYS ILE PHE PHE CYS THR SER GLN ASP ILE PRO SEQRES 11 B 151 PRO GLU ASN GLU LEU LEU PHE TYR TYR SER ARG ASP TYR SEQRES 12 B 151 ALA GLN GLN ILE GLY VAL PRO GLU MODRES 3DB5 MSE A 98 MET SELENOMETHIONINE MODRES 3DB5 MSE A 99 MET SELENOMETHIONINE MODRES 3DB5 MSE B 61 MET SELENOMETHIONINE MODRES 3DB5 MSE B 98 MET SELENOMETHIONINE MODRES 3DB5 MSE B 99 MET SELENOMETHIONINE HET MSE A 98 8 HET MSE A 99 8 HET MSE B 61 5 HET MSE B 98 8 HET MSE B 99 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 3 HOH *139(H2 O) HELIX 1 1 SER A 15 SER A 20 1 6 HELIX 2 2 ASN A 96 VAL A 101 5 6 HELIX 3 3 SER B 15 SER B 20 1 6 HELIX 4 4 ASN B 96 VAL B 101 5 6 HELIX 5 5 SER B 140 GLY B 148 1 9 SHEET 1 A 2 LEU A 25 GLN A 29 0 SHEET 2 A 2 VAL A 36 THR A 40 -1 O TRP A 39 N VAL A 26 SHEET 1 B 5 CYS A 49 PHE A 50 0 SHEET 2 B 5 LYS A 120 THR A 125 -1 O PHE A 123 N PHE A 50 SHEET 3 B 5 LEU A 112 HIS A 117 -1 N HIS A 117 O LYS A 120 SHEET 4 B 5 LEU A 136 TYR A 139 1 O TYR A 138 N ALA A 114 SHEET 5 B 5 ARG A 102 LYS A 103 1 N ARG A 102 O PHE A 137 SHEET 1 C 3 GLN A 56 SER A 58 0 SHEET 2 C 3 VAL A 82 ILE A 88 -1 O CYS A 86 N SER A 58 SHEET 3 C 3 ILE A 74 HIS A 79 -1 N ILE A 77 O PHE A 85 SHEET 1 D 2 LEU B 25 GLN B 29 0 SHEET 2 D 2 VAL B 36 THR B 40 -1 O TRP B 39 N VAL B 26 SHEET 1 E 5 CYS B 49 PHE B 50 0 SHEET 2 E 5 LYS B 120 THR B 125 -1 O PHE B 123 N PHE B 50 SHEET 3 E 5 LEU B 112 HIS B 117 -1 N TYR B 115 O PHE B 122 SHEET 4 E 5 LEU B 136 TYR B 139 1 O TYR B 138 N ALA B 114 SHEET 5 E 5 ARG B 102 LYS B 103 1 N ARG B 102 O PHE B 137 SHEET 1 F 3 GLN B 56 SER B 58 0 SHEET 2 F 3 VAL B 82 ILE B 88 -1 O ILE B 88 N GLN B 56 SHEET 3 F 3 ILE B 74 HIS B 79 -1 N ILE B 77 O GLU B 84 SSBOND 1 CYS B 49 CYS B 124 1555 1555 2.06 LINK C TRP A 97 N MSE A 98 1555 1555 1.32 LINK C MSE A 98 N MSE A 99 1555 1555 1.35 LINK C MSE A 99 N PHE A 100 1555 1555 1.35 LINK C SER B 60 N MSE B 61 1555 1555 1.34 LINK C TRP B 97 N MSE B 98 1555 1555 1.33 LINK C MSE B 98 N MSE B 99 1555 1555 1.33 LINK C MSE B 99 N PHE B 100 1555 1555 1.34 CISPEP 1 GLY A 51 PRO A 52 0 3.63 CISPEP 2 GLY B 51 PRO B 52 0 1.49 CRYST1 107.294 107.294 133.642 90.00 90.00 90.00 I 4 2 2 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 0.009320 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009320 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007483 0.00000