PDB Short entry for 2IMW HEADER TRANSFERASE/DNA 05-OCT-06 2IMW TITLE MECHANISM OF TEMPLATE-INDEPENDENT NUCLEOTIDE INCORPORATION CATALYZED TITLE 2 BY A TEMPLATE-DEPENDENT DNA POLYMERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'; COMPND 3 CHAIN: S; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*TP*AP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'; COMPND 7 CHAIN: T; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA POLYMERASE IV; COMPND 11 CHAIN: P; COMPND 12 SYNONYM: POL IV; COMPND 13 EC: 2.7.7.7; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 7 ORGANISM_TAXID: 2287; SOURCE 8 GENE: DBIN; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BLUNT END DNA Y-FAMILY POLYMERASE DNA REPLICATION, TRANSFERASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.LING,W.YANG REVDAT 8 30-AUG-23 2IMW 1 REMARK LINK REVDAT 7 24-JUL-19 2IMW 1 REMARK LINK REVDAT 6 04-APR-18 2IMW 1 REMARK REVDAT 5 18-OCT-17 2IMW 1 REMARK REVDAT 4 13-JUL-11 2IMW 1 VERSN REVDAT 3 23-JUN-10 2IMW 1 HET REVDAT 2 24-FEB-09 2IMW 1 VERSN REVDAT 1 16-JAN-07 2IMW 0 JRNL AUTH K.A.FIALA,J.A.BROWN,H.LING,A.K.KSHETRY,J.ZHANG,J.S.TAYLOR, JRNL AUTH 2 W.YANG,Z.SUO JRNL TITL MECHANISM OF TEMPLATE-INDEPENDENT NUCLEOTIDE INCORPORATION JRNL TITL 2 CATALYZED BY A TEMPLATE-DEPENDENT DNA POLYMERASE. JRNL REF J.MOL.BIOL. V. 365 590 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17095011 JRNL DOI 10.1016/J.JMB.2006.10.008 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 32833 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) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.900 REMARK 3 FREE R VALUE TEST SET COUNT : 954 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2246 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3350 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.3840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2788 REMARK 3 NUCLEIC ACID ATOMS : 568 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 240 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) : 45.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.66000 REMARK 3 B22 (A**2) : -1.89000 REMARK 3 B33 (A**2) : -0.76000 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): 0.221 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.200 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.151 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.169 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3556 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4904 ; 1.303 ; 2.206 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 357 ; 4.618 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;32.880 ;23.689 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 579 ;14.592 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;12.457 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 557 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2387 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1571 ; 0.223 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2400 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 274 ; 0.176 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 8 ; 0.148 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 51 ; 0.167 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.207 ; 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): 1837 ; 1.231 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2872 ; 1.372 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2138 ; 2.500 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2032 ; 3.114 ; 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 : 5 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 : P 11 P 77 REMARK 3 ORIGIN FOR THE GROUP (A): 13.7824 6.9558 31.1285 REMARK 3 T TENSOR REMARK 3 T11: -0.0241 T22: 0.0269 REMARK 3 T33: -0.0496 T12: 0.0086 REMARK 3 T13: -0.0007 T23: -0.0273 REMARK 3 L TENSOR REMARK 3 L11: 0.5251 L22: 0.3165 REMARK 3 L33: 1.6291 L12: 0.3743 REMARK 3 L13: 0.8032 L23: 0.4315 REMARK 3 S TENSOR REMARK 3 S11: 0.0115 S12: 0.1226 S13: 0.0181 REMARK 3 S21: 0.0629 S22: 0.0120 S23: -0.0246 REMARK 3 S31: 0.0722 S32: -0.1446 S33: -0.0234 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 : P 167 P 240 REMARK 3 ORIGIN FOR THE GROUP (A): 31.9976 30.5361 36.5130 REMARK 3 T TENSOR REMARK 3 T11: -0.0557 T22: 0.0081 REMARK 3 T33: -0.0203 T12: -0.0603 REMARK 3 T13: -0.0708 T23: 0.1249 REMARK 3 L TENSOR REMARK 3 L11: 2.1200 L22: 1.2882 REMARK 3 L33: 0.9678 L12: 0.9309 REMARK 3 L13: -0.6497 L23: -0.2711 REMARK 3 S TENSOR REMARK 3 S11: -0.2242 S12: 0.3791 S13: 0.3208 REMARK 3 S21: -0.1406 S22: 0.1456 S23: -0.0744 REMARK 3 S31: -0.1063 S32: -0.0388 S33: 0.0787 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : P 1 P 10 REMARK 3 RESIDUE RANGE : P 78 P 166 REMARK 3 ORIGIN FOR THE GROUP (A): 34.8293 9.2886 37.2790 REMARK 3 T TENSOR REMARK 3 T11: -0.0823 T22: -0.0027 REMARK 3 T33: 0.0489 T12: 0.0244 REMARK 3 T13: 0.0082 T23: -0.0383 REMARK 3 L TENSOR REMARK 3 L11: 0.8182 L22: 1.6869 REMARK 3 L33: 0.8981 L12: 0.7965 REMARK 3 L13: 0.6952 L23: 0.5021 REMARK 3 S TENSOR REMARK 3 S11: 0.0415 S12: 0.3062 S13: -0.2857 REMARK 3 S21: 0.0220 S22: 0.0814 S23: -0.4485 REMARK 3 S31: 0.1031 S32: 0.2188 S33: -0.1228 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 : P 241 P 341 REMARK 3 ORIGIN FOR THE GROUP (A): 7.3915 16.8803 55.5273 REMARK 3 T TENSOR REMARK 3 T11: -0.0767 T22: -0.0205 REMARK 3 T33: -0.0474 T12: -0.0324 REMARK 3 T13: 0.0239 T23: -0.0203 REMARK 3 L TENSOR REMARK 3 L11: 2.9984 L22: 2.4153 REMARK 3 L33: 3.1295 L12: 0.5440 REMARK 3 L13: 1.1849 L23: -1.0380 REMARK 3 S TENSOR REMARK 3 S11: -0.0754 S12: -0.0070 S13: 0.1917 REMARK 3 S21: -0.1755 S22: -0.0314 S23: 0.1086 REMARK 3 S31: 0.2352 S32: -0.2611 S33: 0.1068 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : S 1801 S 1813 REMARK 3 RESIDUE RANGE : T 1906 T 1918 REMARK 3 ORIGIN FOR THE GROUP (A): 20.6197 30.1288 52.8737 REMARK 3 T TENSOR REMARK 3 T11: 0.0898 T22: -0.0976 REMARK 3 T33: -0.0140 T12: -0.0242 REMARK 3 T13: -0.0750 T23: -0.0197 REMARK 3 L TENSOR REMARK 3 L11: 0.7319 L22: 1.3856 REMARK 3 L33: 0.9870 L12: 0.2012 REMARK 3 L13: -0.6020 L23: 0.6433 REMARK 3 S TENSOR REMARK 3 S11: 0.0181 S12: 0.0393 S13: 0.1101 REMARK 3 S21: -0.0066 S22: -0.1485 S23: -0.2093 REMARK 3 S31: 0.0784 S32: -0.2097 S33: 0.1303 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2IMW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039764. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-02 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 7.0 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRRORS 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 : 32881 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.34000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY: 1JX4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG3350, 0.1 M CALCIUM ACETATE, REMARK 280 0.1 M HEPES PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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 -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 49.02850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.92850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.02850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.92850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: S, T, P 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 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 GLU P 342 CG CD OE1 OE2 REMARK 470 ASP P 347 CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH P 542 O HOH P 643 1.95 REMARK 500 REMARK 500 REMARK: NULL 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 DC T1917 O3' DC T1917 C3' -0.036 REMARK 500 GLU P 79 CD GLU P 79 OE2 0.069 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 DG S1803 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG S1805 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT T1904 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA T1907 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT T1909 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC T1910 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC T1911 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT T1912 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC T1917 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 DC T1917 O4' - C1' - N1 ANGL. DEV. = 3.4 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 TYR P 10 52.83 27.77 REMARK 500 ASP P 39 18.43 58.55 REMARK 500 SER P 145 -167.14 -165.70 REMARK 500 ASN P 161 50.73 39.00 REMARK 500 GLU P 235 120.23 -28.77 REMARK 500 ASP P 277 -108.34 58.68 REMARK 500 GLU P 342 7.45 114.30 REMARK 500 ALA P 343 -166.35 -176.67 REMARK 500 ASP P 347 152.38 164.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA P 407 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH T 50 O REMARK 620 2 HOH T 193 O 91.2 REMARK 620 3 ALA P 181 O 82.1 172.5 REMARK 620 4 ILE P 186 O 76.0 88.8 86.3 REMARK 620 5 HOH P 663 O 147.7 92.7 91.3 72.1 REMARK 620 6 HOH P 669 O 69.8 91.3 89.5 145.8 142.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA P 406 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP P 7 OD1 REMARK 620 2 PHE P 8 O 87.1 REMARK 620 3 ASP P 105 OD2 98.4 91.7 REMARK 620 4 DDS P 401 O2B 177.5 90.9 83.2 REMARK 620 5 DDS P 401 O1G 99.6 123.6 140.9 80.2 REMARK 620 6 HOH P 660 O 79.6 158.9 74.4 102.8 75.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA P 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA P 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDS P 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO P 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO P 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO P 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO P 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO P 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO P 506 DBREF 2IMW P 1 348 UNP Q97W02 DPO42_SULSO 1 348 DBREF 2IMW S 1801 1813 PDB 2IMW 2IMW 1801 1813 DBREF 2IMW T 1904 1918 PDB 2IMW 2IMW 1904 1918 SEQRES 1 S 13 DG DG DG DG DG DA DA DG DG DA DT DT DC SEQRES 1 T 15 DT DA DG DA DA DT DC DC DT DT DC DC DC SEQRES 2 T 15 DC DC SEQRES 1 P 348 MET ILE VAL LEU PHE VAL ASP PHE ASP TYR PHE TYR ALA SEQRES 2 P 348 GLN VAL GLU GLU VAL LEU ASN PRO SER LEU LYS GLY LYS SEQRES 3 P 348 PRO VAL VAL VAL CYS VAL PHE SER GLY ARG PHE GLU ASP SEQRES 4 P 348 SER GLY ALA VAL ALA THR ALA ASN TYR GLU ALA ARG LYS SEQRES 5 P 348 PHE GLY VAL LYS ALA GLY ILE PRO ILE VAL GLU ALA LYS SEQRES 6 P 348 LYS ILE LEU PRO ASN ALA VAL TYR LEU PRO MET ARG LYS SEQRES 7 P 348 GLU VAL TYR GLN GLN VAL SER SER ARG ILE MET ASN LEU SEQRES 8 P 348 LEU ARG GLU TYR SER GLU LYS ILE GLU ILE ALA SER ILE SEQRES 9 P 348 ASP GLU ALA TYR LEU ASP ILE SER ASP LYS VAL ARG ASP SEQRES 10 P 348 TYR ARG GLU ALA TYR ASN LEU GLY LEU GLU ILE LYS ASN SEQRES 11 P 348 LYS ILE LEU GLU LYS GLU LYS ILE THR VAL THR VAL GLY SEQRES 12 P 348 ILE SER LYS ASN LYS VAL PHE ALA LYS ILE ALA ALA ASP SEQRES 13 P 348 MET ALA LYS PRO ASN GLY ILE LYS VAL ILE ASP ASP GLU SEQRES 14 P 348 GLU VAL LYS ARG LEU ILE ARG GLU LEU ASP ILE ALA ASP SEQRES 15 P 348 VAL PRO GLY ILE GLY ASN ILE THR ALA GLU LYS LEU LYS SEQRES 16 P 348 LYS LEU GLY ILE ASN LYS LEU VAL ASP THR LEU SER ILE SEQRES 17 P 348 GLU PHE ASP LYS LEU LYS GLY MET ILE GLY GLU ALA LYS SEQRES 18 P 348 ALA LYS TYR LEU ILE SER LEU ALA ARG ASP GLU TYR ASN SEQRES 19 P 348 GLU PRO ILE ARG THR ARG VAL ARG LYS SER ILE GLY ARG SEQRES 20 P 348 ILE VAL THR MET LYS ARG ASN SER ARG ASN LEU GLU GLU SEQRES 21 P 348 ILE LYS PRO TYR LEU PHE ARG ALA ILE GLU GLU SER TYR SEQRES 22 P 348 TYR LYS LEU ASP LYS ARG ILE PRO LYS ALA ILE HIS VAL SEQRES 23 P 348 VAL ALA VAL THR GLU ASP LEU ASP ILE VAL SER ARG GLY SEQRES 24 P 348 ARG THR PHE PRO HIS GLY ILE SER LYS GLU THR ALA TYR SEQRES 25 P 348 SER GLU SER VAL LYS LEU LEU GLN LYS ILE LEU GLU GLU SEQRES 26 P 348 ASP GLU ARG LYS ILE ARG ARG ILE GLY VAL ARG PHE SER SEQRES 27 P 348 LYS PHE ILE GLU ALA ILE GLY LEU ASP LYS HET CA P 406 1 HET CA P 407 1 HET DDS P 401 29 HET EDO P 501 4 HET EDO P 502 4 HET EDO P 503 4 HET EDO P 504 4 HET EDO P 505 4 HET EDO P 506 4 HETNAM CA CALCIUM ION HETNAM DDS 2',3'-DIDEOXYADENOSINE TRIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 CA 2(CA 2+) FORMUL 6 DDS C10 H16 N5 O11 P3 FORMUL 7 EDO 6(C2 H6 O2) FORMUL 13 HOH *240(H2 O) HELIX 1 1 TYR P 10 ASN P 20 1 11 HELIX 2 2 PRO P 21 LYS P 24 5 4 HELIX 3 3 ASN P 47 LYS P 52 1 6 HELIX 4 4 PRO P 60 LEU P 68 1 9 HELIX 5 5 ARG P 77 ARG P 93 1 17 HELIX 6 6 ASP P 117 LYS P 137 1 21 HELIX 7 7 ASN P 147 LYS P 159 1 13 HELIX 8 8 ASP P 167 LEU P 178 1 12 HELIX 9 9 ASP P 179 VAL P 183 5 5 HELIX 10 10 GLY P 187 LYS P 196 1 10 HELIX 11 11 LYS P 201 SER P 207 5 7 HELIX 12 12 GLU P 209 GLY P 218 1 10 HELIX 13 13 GLY P 218 ARG P 230 1 13 HELIX 14 14 ASN P 257 ASP P 277 1 21 HELIX 15 15 SER P 307 ASP P 326 1 20 SHEET 1 A 5 ILE P 99 SER P 103 0 SHEET 2 A 5 GLU P 106 ASP P 110 -1 O TYR P 108 N GLU P 100 SHEET 3 A 5 VAL P 3 PHE P 8 -1 N LEU P 4 O LEU P 109 SHEET 4 A 5 VAL P 140 SER P 145 -1 O SER P 145 N VAL P 3 SHEET 5 A 5 ILE P 163 VAL P 165 1 O LYS P 164 N ILE P 144 SHEET 1 B 3 GLY P 41 ALA P 46 0 SHEET 2 B 3 VAL P 28 PHE P 33 -1 N VAL P 32 O ALA P 42 SHEET 3 B 3 VAL P 72 PRO P 75 1 O LEU P 74 N CYS P 31 SHEET 1 C 4 SER P 244 SER P 255 0 SHEET 2 C 4 ILE P 330 PHE P 340 -1 O PHE P 337 N ILE P 245 SHEET 3 C 4 PRO P 281 THR P 290 -1 N VAL P 289 O ARG P 331 SHEET 4 C 4 ILE P 295 THR P 301 -1 O VAL P 296 N ALA P 288 LINK NZ LYS P 78 O2 EDO P 502 1555 1555 1.99 LINK O HOH T 50 CA CA P 407 1555 1555 2.75 LINK O HOH T 193 CA CA P 407 1555 1555 2.46 LINK OD1 ASP P 7 CA CA P 406 1555 1555 2.27 LINK O PHE P 8 CA CA P 406 1555 1555 2.33 LINK OD2 ASP P 105 CA CA P 406 1555 1555 2.30 LINK O ALA P 181 CA CA P 407 1555 1555 2.35 LINK O ILE P 186 CA CA P 407 1555 1555 2.51 LINK O2B DDS P 401 CA CA P 406 1555 1555 2.36 LINK O1G DDS P 401 CA CA P 406 1555 1555 2.22 LINK CA CA P 406 O HOH P 660 1555 1555 2.48 LINK CA CA P 407 O HOH P 663 1555 1555 2.31 LINK CA CA P 407 O HOH P 669 1555 1555 2.15 CISPEP 1 LYS P 159 PRO P 160 0 -0.74 SITE 1 AC1 5 ASP P 7 PHE P 8 ASP P 105 DDS P 401 SITE 2 AC1 5 HOH P 660 SITE 1 AC2 6 ALA P 181 ILE P 186 HOH P 663 HOH P 669 SITE 2 AC2 6 HOH T 50 HOH T 193 SITE 1 AC3 22 ASP P 7 PHE P 8 ASP P 9 TYR P 10 SITE 2 AC3 22 PHE P 11 ALA P 44 THR P 45 TYR P 48 SITE 3 AC3 22 ARG P 51 ASP P 105 LYS P 159 CA P 406 SITE 4 AC3 22 HOH P 508 HOH P 509 HOH P 513 HOH P 613 SITE 5 AC3 22 HOH P 660 HOH P 665 HOH P 670 HOH P 672 SITE 6 AC3 22 DG S1801 DC T1918 SITE 1 AC4 4 GLU P 100 LYS P 148 ARG P 240 HOH S 206 SITE 1 AC5 3 LYS P 78 ARG P 247 DG S1802 SITE 1 AC6 2 ALA P 220 TYR P 224 SITE 1 AC7 5 HIS P 285 VAL P 287 SER P 297 ARG P 336 SITE 2 AC7 5 LYS P 348 SITE 1 AC8 1 TYR P 122 SITE 1 AC9 3 VAL P 249 ARG P 267 GLU P 271 CRYST1 98.057 101.857 52.380 90.00 90.00 90.00 P 21 21 2 4 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 0.010198 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009818 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019091 0.00000