HEADER REPLICATION 20-SEP-25 9YD2 TITLE TERNARY COMPLEX OF DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS, TITLE 2 LARGE FRAGMENT, BOUND TO DNA CONTAINING A THYMINE DIMER AND DATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*AP*AP*GP*GP*AP*CP*AP*GP*TP*(DDG))-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*AP*(TTD)P*CP*AP*CP*TP*GP*TP*CP*CP*TP*TP*G)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 GENE: DPO1, POLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS POLYMERASE, COMPLEX, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR E.Y.WU,A.R.WALSH REVDAT 1 24-JUN-26 9YD2 0 JRNL AUTH A.R.WALSH,L.S.BEESE,E.Y.WU JRNL TITL STRUCTURAL BASIS FOR BLOCKAGE OF DNA SYNTHESIS BY A THYMINE JRNL TITL 2 DIMER LESION IN A HIGH-FIDELITY DNA POLYMERASE JRNL REF BIOCHEMISTRY 2026 JRNL REFN ISSN 0006-2960 JRNL DOI 10.1021/ACS.BIOCHEM.5C00781 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 44763 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.299 REMARK 3 FREE R VALUE TEST SET COUNT : 2372 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2885 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.4100 REMARK 3 BIN FREE R VALUE SET COUNT : 137 REMARK 3 BIN FREE R VALUE : 0.4040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4651 REMARK 3 NUCLEIC ACID ATOMS : 505 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 98 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00100 REMARK 3 B22 (A**2) : 0.00100 REMARK 3 B33 (A**2) : -0.00400 REMARK 3 B12 (A**2) : 0.00100 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): 0.258 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.232 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.215 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.217 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5349 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4932 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7341 ; 1.948 ; 1.844 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11365 ; 0.642 ; 1.760 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 581 ; 7.054 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 44 ; 9.683 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 876 ;16.610 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 828 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5898 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1161 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1155 ; 0.241 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 50 ; 0.145 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2540 ; 0.190 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 173 ; 0.180 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.036 ; 0.200 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2321 ; 5.889 ; 5.347 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2321 ; 5.888 ; 5.348 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2900 ; 8.319 ; 9.594 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2901 ; 8.319 ; 9.595 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3028 ; 7.122 ; 6.480 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3016 ; 7.077 ; 6.470 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4438 ;10.642 ;11.698 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4421 ;10.575 ;11.683 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9YD2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1000300284. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44763 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.249 REMARK 200 RESOLUTION RANGE LOW (A) : 79.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.420 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 46% (V/V) SATURATED AMMONIUM SULFATE, REMARK 280 10 MM MANGANESE SULFATE (MNSO4), 100 MM 2-(N-MORPHOLINO) REMARK 280 ETHANESULFONIC ACID (MES), 5% 2-METHYL-1,3-PROPANEDIOL (MPD), 1 REMARK 280 MM 2',3'-DIDEOXYGUANOSINE TRIPHOSPHATE, 5 MM 2'-DEOXYADENOSINE REMARK 280 TRIPHOSPHATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.23000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 126.46000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 126.46000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.23000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 MET A 296 REMARK 465 DA C 15 REMARK 465 DC C 16 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 OG SER A 643 OE2 GLU A 835 2.14 REMARK 500 OH TYR A 419 O HOH A 1001 2.17 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 MET A 488 CG - SD - CE ANGL. DEV. = 10.1 DEGREES REMARK 500 GLU A 644 CB - CA - C ANGL. DEV. = -13.3 DEGREES REMARK 500 MET A 672 CG - SD - CE ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 677 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 LYS A 706 CB - CA - C ANGL. DEV. = -13.2 DEGREES REMARK 500 MET A 808 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 DC B 25 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA B 26 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 27 O5' - P - OP2 ANGL. DEV. = -6.0 DEGREES REMARK 500 DDG B 29 O3' - P - O5' ANGL. DEV. = 19.0 DEGREES REMARK 500 DA C 2 C1' - O4' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 DA C 2 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 DA C 2 C3' - O3' - P ANGL. DEV. = 22.4 DEGREES REMARK 500 TTD C 3 O3' - P - OP2 ANGL. DEV. = -14.9 DEGREES REMARK 500 TTD C 3 O3' - P - OP1 ANGL. DEV. = 16.6 DEGREES REMARK 500 TTD C 3 C3' - O3' - P ANGL. DEV. = -11.5 DEGREES REMARK 500 DC C 4 O3' - P - O5' ANGL. DEV. = -14.5 DEGREES REMARK 500 DC C 4 O3' - P - OP1 ANGL. DEV. = 32.3 DEGREES REMARK 500 DC C 4 OP1 - P - OP2 ANGL. DEV. = -11.2 DEGREES REMARK 500 DC C 4 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES REMARK 500 DC C 6 O5' - P - OP2 ANGL. DEV. = -7.0 DEGREES REMARK 500 DC C 6 O5' - C5' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 DC C 6 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT C 7 O3' - P - O5' ANGL. DEV. = 11.4 DEGREES REMARK 500 DC C 10 O3' - P - O5' ANGL. DEV. = -12.0 DEGREES REMARK 500 DC C 10 O5' - P - OP2 ANGL. DEV. = 9.3 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 LEU A 303 77.40 -69.41 REMARK 500 THR A 350 -62.14 -93.93 REMARK 500 ASP A 372 61.11 60.52 REMARK 500 ASP A 402 96.59 -160.00 REMARK 500 GLN A 418 32.91 76.32 REMARK 500 ALA A 421 38.79 -79.78 REMARK 500 LEU A 477 -65.33 -125.44 REMARK 500 GLU A 520 -71.63 -48.72 REMARK 500 GLN A 524 168.88 176.64 REMARK 500 VAL A 536 -70.78 -59.94 REMARK 500 THR A 550 -130.60 -105.60 REMARK 500 TYR A 587 -63.19 -94.98 REMARK 500 LEU A 610 -58.38 -127.76 REMARK 500 GLU A 620 70.90 44.42 REMARK 500 ILE A 628 -26.02 -142.65 REMARK 500 ASP A 646 18.15 82.04 REMARK 500 ILE A 689 -70.24 -115.19 REMARK 500 PHE A 690 21.65 -78.29 REMARK 500 GLN A 691 80.23 19.40 REMARK 500 TYR A 719 -77.14 -55.14 REMARK 500 ASN A 726 18.22 82.39 REMARK 500 PHE A 743 69.00 -118.03 REMARK 500 HIS A 829 -54.04 71.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 306 0.08 SIDE CHAIN REMARK 500 ARG A 435 0.09 SIDE CHAIN REMARK 500 ARG A 789 0.14 SIDE CHAIN 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 MN A 902 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DTP A 901 O3G REMARK 620 2 DTP A 901 O1B 85.2 REMARK 620 3 DTP A 901 O1A 92.3 72.2 REMARK 620 N 1 2 DBREF 9YD2 A 298 876 UNP D9N168 D9N168_GEOSE 1 579 DBREF 9YD2 B 19 29 PDB 9YD2 9YD2 19 29 DBREF 9YD2 C 2 16 PDB 9YD2 9YD2 2 16 SEQADV 9YD2 MET A 296 UNP D9N168 INITIATING METHIONINE SEQADV 9YD2 ALA A 297 UNP D9N168 EXPRESSION TAG SEQADV 9YD2 VAL A 713 UNP D9N168 PRO 416 CONFLICT SEQRES 1 A 581 MET ALA LYS MET ALA PHE THR LEU ALA ASP ARG VAL THR SEQRES 2 A 581 GLU GLU MET LEU ALA ASP LYS ALA ALA LEU VAL VAL GLU SEQRES 3 A 581 VAL VAL GLU GLU ASN TYR HIS ASP ALA PRO ILE VAL GLY SEQRES 4 A 581 ILE ALA VAL VAL ASN GLU HIS GLY ARG PHE PHE LEU ARG SEQRES 5 A 581 PRO GLU THR ALA LEU ALA ASP PRO GLN PHE VAL ALA TRP SEQRES 6 A 581 LEU GLY ASP GLU THR LYS LYS LYS SER MET PHE ASP SER SEQRES 7 A 581 LYS ARG ALA ALA VAL ALA LEU LYS TRP LYS GLY ILE GLU SEQRES 8 A 581 LEU CYS GLY VAL SER PHE ASP LEU LEU LEU ALA ALA TYR SEQRES 9 A 581 LEU LEU ASP PRO ALA GLN GLY VAL ASP ASP VAL ALA ALA SEQRES 10 A 581 ALA ALA LYS MET LYS GLN TYR GLU ALA VAL ARG PRO ASP SEQRES 11 A 581 GLU ALA VAL TYR GLY LYS GLY ALA LYS ARG ALA VAL PRO SEQRES 12 A 581 ASP GLU PRO VAL LEU ALA GLU HIS LEU VAL ARG LYS ALA SEQRES 13 A 581 ALA ALA ILE TRP GLU LEU GLU ARG PRO PHE LEU ASP GLU SEQRES 14 A 581 LEU ARG ARG ASN GLU GLN ASP ARG LEU LEU VAL GLU LEU SEQRES 15 A 581 GLU GLN PRO LEU SER SER ILE LEU ALA GLU MET GLU PHE SEQRES 16 A 581 ALA GLY VAL LYS VAL ASP THR LYS ARG LEU GLU GLN MET SEQRES 17 A 581 GLY LYS GLU LEU ALA GLU GLN LEU GLY THR VAL GLU GLN SEQRES 18 A 581 ARG ILE TYR GLU LEU ALA GLY GLN GLU PHE ASN ILE ASN SEQRES 19 A 581 SER PRO LYS GLN LEU GLY VAL ILE LEU PHE GLU LYS LEU SEQRES 20 A 581 GLN LEU PRO VAL LEU LYS LYS THR LYS THR GLY TYR SER SEQRES 21 A 581 THR SER ALA ASP VAL LEU GLU LYS LEU ALA PRO TYR HIS SEQRES 22 A 581 GLU ILE VAL GLU ASN ILE LEU HIS TYR ARG GLN LEU GLY SEQRES 23 A 581 LYS LEU GLN SER THR TYR ILE GLU GLY LEU LEU LYS VAL SEQRES 24 A 581 VAL ARG PRO ALA THR LYS LYS VAL HIS THR ILE PHE ASN SEQRES 25 A 581 GLN ALA LEU THR GLN THR GLY ARG LEU SER SER THR GLU SEQRES 26 A 581 PRO ASN LEU GLN ASN ILE PRO ILE ARG LEU GLU GLU GLY SEQRES 27 A 581 ARG LYS ILE ARG GLN ALA PHE VAL PRO SER GLU SER ASP SEQRES 28 A 581 TRP LEU ILE PHE ALA ALA ASP TYR SER GLN ILE GLU LEU SEQRES 29 A 581 ARG VAL LEU ALA HIS ILE ALA GLU ASP ASP ASN LEU MET SEQRES 30 A 581 GLU ALA PHE ARG ARG ASP LEU ASP ILE HIS THR LYS THR SEQRES 31 A 581 ALA MET ASP ILE PHE GLN VAL SER GLU ASP GLU VAL THR SEQRES 32 A 581 PRO ASN MET ARG ARG GLN ALA LYS ALA VAL ASN PHE GLY SEQRES 33 A 581 ILE VAL TYR GLY ILE SER ASP TYR GLY LEU ALA GLN ASN SEQRES 34 A 581 LEU ASN ILE SER ARG LYS GLU ALA ALA GLU PHE ILE GLU SEQRES 35 A 581 ARG TYR PHE GLU SER PHE PRO GLY VAL LYS ARG TYR MET SEQRES 36 A 581 GLU ASN ILE VAL GLN GLU ALA LYS GLN LYS GLY TYR VAL SEQRES 37 A 581 THR THR LEU LEU HIS ARG ARG ARG TYR LEU PRO ASP ILE SEQRES 38 A 581 THR SER ARG ASN PHE ASN VAL ARG SER PHE ALA GLU ARG SEQRES 39 A 581 MET ALA MET ASN THR PRO ILE GLN GLY SER ALA ALA ASP SEQRES 40 A 581 ILE ILE LYS LYS ALA MET ILE ASP LEU ASN ALA ARG LEU SEQRES 41 A 581 LYS GLU GLU ARG LEU GLN ALA HIS LEU LEU LEU GLN VAL SEQRES 42 A 581 HIS ASP GLU LEU ILE LEU GLU ALA PRO LYS GLU GLU MET SEQRES 43 A 581 GLU ARG LEU CYS ARG LEU VAL PRO GLU VAL MET GLU GLN SEQRES 44 A 581 ALA VAL THR LEU ARG VAL PRO LEU LYS VAL ASP TYR HIS SEQRES 45 A 581 TYR GLY SER THR TRP TYR ASP ALA LYS SEQRES 1 B 11 DC DA DA DG DG DA DC DA DG DT DDG SEQRES 1 C 15 DA TTD DC DA DC DT DG DT DC DC DT DT DG SEQRES 2 C 15 DA DC HET DDG B 29 21 HET TTD C 3 40 HET DTP A 901 30 HET MN A 902 1 HET SO4 A 903 5 HET SO4 A 904 5 HET SO4 A 905 5 HETNAM DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM TTD CIS-SYN CYCLOBUTANE THYMINE DIMER HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM SO4 SULFATE ION HETSYN TTD [(3S,4S,9S,10R,12R,15AR,18BS,18CS)-3,7-DIHYDROXY-15A, HETSYN 2 TTD 15B-DIMETHYL-7-OXIDO-13,15,16,18- HETSYN 3 TTD TETRAOXOHEXADECAHYDRO-1H-1,4-EPOX Y-9,12-METHANO-6,8, HETSYN 4 TTD 11-TRIOXA-12A,14,17,18A-TETRAAZA-7- HETSYN 5 TTD PHOSPHACYCLOHEXADECA[1,2,3,4-DEF]BIPHENYLEN-10- HETSYN 6 TTD YL]METHYL DIHYDROGEN PHOSPHATE FORMUL 2 DDG C10 H14 N5 O6 P FORMUL 3 TTD C20 H28 N4 O15 P2 FORMUL 4 DTP C10 H16 N5 O12 P3 FORMUL 5 MN MN 2+ FORMUL 6 SO4 3(O4 S 2-) FORMUL 9 HOH *98(H2 O) HELIX 1 AA1 THR A 308 ALA A 313 5 6 HELIX 2 AA2 ARG A 347 LEU A 352 1 6 HELIX 3 AA3 ASP A 354 ASP A 363 1 10 HELIX 4 AA4 ASP A 372 TRP A 382 1 11 HELIX 5 AA5 LEU A 394 ASP A 402 1 9 HELIX 6 AA6 PRO A 403 GLY A 406 5 4 HELIX 7 AA7 ASP A 409 MET A 416 1 8 HELIX 8 AA8 PRO A 424 GLY A 430 1 7 HELIX 9 AA9 ASP A 439 ASN A 468 1 30 HELIX 10 AB1 GLN A 470 GLU A 476 1 7 HELIX 11 AB2 LEU A 477 GLY A 492 1 16 HELIX 12 AB3 ASP A 496 GLY A 523 1 28 HELIX 13 AB4 SER A 530 GLU A 540 1 11 HELIX 14 AB5 SER A 557 LEU A 564 1 8 HELIX 15 AB6 GLU A 569 THR A 586 1 18 HELIX 16 AB7 TYR A 587 VAL A 595 1 9 HELIX 17 AB8 LEU A 630 LYS A 635 1 6 HELIX 18 AB9 ILE A 636 GLN A 638 5 3 HELIX 19 AC1 GLN A 656 GLU A 667 1 12 HELIX 20 AC2 ASP A 668 ARG A 677 1 10 HELIX 21 AC3 ASP A 680 PHE A 690 1 11 HELIX 22 AC4 SER A 693 VAL A 697 5 5 HELIX 23 AC5 THR A 698 TYR A 714 1 17 HELIX 24 AC6 SER A 717 ASN A 726 1 10 HELIX 25 AC7 SER A 728 PHE A 743 1 16 HELIX 26 AC8 PHE A 743 GLY A 761 1 19 HELIX 27 AC9 PRO A 774 SER A 778 5 5 HELIX 28 AD1 ASN A 780 GLU A 818 1 39 HELIX 29 AD2 GLU A 840 ALA A 855 1 16 SHEET 1 AA1 6 THR A 302 LEU A 303 0 SHEET 2 AA1 6 GLY A 342 LEU A 346 1 O ARG A 343 N THR A 302 SHEET 3 AA1 6 GLY A 334 ASN A 339 -1 N ILE A 335 O LEU A 346 SHEET 4 AA1 6 LYS A 315 GLU A 321 -1 N VAL A 319 O ALA A 336 SHEET 5 AA1 6 LYS A 367 MET A 370 1 O SER A 369 N ALA A 316 SHEET 6 AA1 6 VAL A 390 ASP A 393 1 O PHE A 392 N MET A 370 SHEET 1 AA2 3 LYS A 601 VAL A 602 0 SHEET 2 AA2 3 VAL A 493 VAL A 495 -1 N VAL A 493 O VAL A 602 SHEET 3 AA2 3 PHE A 640 VAL A 641 -1 O VAL A 641 N LYS A 494 SHEET 1 AA3 2 ILE A 605 ASN A 607 0 SHEET 2 AA3 2 SER A 617 THR A 619 -1 O SER A 617 N ASN A 607 SHEET 1 AA4 4 HIS A 823 GLN A 827 0 SHEET 2 AA4 4 GLU A 831 PRO A 837 -1 O ILE A 833 N LEU A 825 SHEET 3 AA4 4 TRP A 647 TYR A 654 -1 N PHE A 650 O LEU A 834 SHEET 4 AA4 4 VAL A 864 GLY A 869 -1 O GLY A 869 N ILE A 649 SHEET 1 AA5 2 TYR A 762 THR A 764 0 SHEET 2 AA5 2 ARG A 770 TYR A 772 -1 O ARG A 771 N VAL A 763 LINK O3' DT B 28 P DDG B 29 1555 1555 1.62 LINK O3' DA C 2 P TTD C 3 1555 1555 1.61 LINK O3' TTD C 3 P DC C 4 1555 1555 1.59 LINK O3G DTP A 901 MN MN A 902 1555 1555 2.18 LINK O1B DTP A 901 MN MN A 902 1555 1555 2.21 LINK O1A DTP A 901 MN MN A 902 1555 1555 2.78 CISPEP 1 GLU A 620 PRO A 621 0 -9.52 CRYST1 92.140 92.140 189.690 90.00 90.00 120.00 P 31 2 1 6 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 0.010853 0.006266 0.000000 0.00000 SCALE2 0.000000 0.012532 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005272 0.00000 CONECT 4849 4861 CONECT 4861 4849 4862 4863 4864 CONECT 4862 4861 CONECT 4863 4861 CONECT 4864 4861 4865 CONECT 4865 4864 4866 CONECT 4866 4865 4867 4868 CONECT 4867 4866 4870 CONECT 4868 4866 4869 CONECT 4869 4868 4870 CONECT 4870 4867 4869 4871 CONECT 4871 4870 4872 4881 CONECT 4872 4871 4873 CONECT 4873 4872 4874 CONECT 4874 4873 4875 4881 CONECT 4875 4874 4876 4877 CONECT 4876 4875 CONECT 4877 4875 4878 CONECT 4878 4877 4879 4880 CONECT 4879 4878 CONECT 4880 4878 4881 CONECT 4881 4871 4874 4880 CONECT 4888 4901 CONECT 4901 4888 4902 4903 4904 CONECT 4902 4901 CONECT 4903 4901 CONECT 4904 4901 4905 CONECT 4905 4904 4906 CONECT 4906 4905 4907 4908 CONECT 4907 4906 4911 CONECT 4908 4906 4909 4910 CONECT 4909 4908 4921 CONECT 4910 4908 4911 CONECT 4911 4907 4910 4912 CONECT 4912 4911 4913 4920 CONECT 4913 4912 4914 4915 CONECT 4914 4913 CONECT 4915 4913 4916 CONECT 4916 4915 4917 4918 CONECT 4917 4916 CONECT 4918 4916 4919 4920 4935 CONECT 4919 4918 CONECT 4920 4912 4918 4937 CONECT 4921 4909 4922 4923 4924 CONECT 4922 4921 CONECT 4923 4921 CONECT 4924 4921 4925 CONECT 4925 4924 4938 CONECT 4926 4928 4938 CONECT 4927 4928 4939 CONECT 4928 4926 4927 4929 CONECT 4929 4928 4930 4937 CONECT 4930 4929 4931 4932 CONECT 4931 4930 CONECT 4932 4930 4933 CONECT 4933 4932 4934 4935 CONECT 4934 4933 CONECT 4935 4918 4933 4936 4937 CONECT 4936 4935 CONECT 4937 4920 4929 4935 CONECT 4938 4925 4926 4939 CONECT 4939 4927 4938 4940 CONECT 4940 4939 4941 CONECT 4941 4940 CONECT 5163 5164 5165 5166 5170 CONECT 5164 5163 CONECT 5165 5163 CONECT 5166 5163 5193 CONECT 5167 5168 5169 5170 5174 CONECT 5168 5167 5193 CONECT 5169 5167 CONECT 5170 5163 5167 CONECT 5171 5172 5173 5174 5175 CONECT 5172 5171 5193 CONECT 5173 5171 CONECT 5174 5167 5171 CONECT 5175 5171 5176 CONECT 5176 5175 5177 CONECT 5177 5176 5178 5179 CONECT 5178 5177 5182 CONECT 5179 5177 5180 5181 CONECT 5180 5179 CONECT 5181 5179 5182 CONECT 5182 5178 5181 5183 CONECT 5183 5182 5184 5192 CONECT 5184 5183 5185 CONECT 5185 5184 5186 CONECT 5186 5185 5187 5192 CONECT 5187 5186 5188 5189 CONECT 5188 5187 CONECT 5189 5187 5190 CONECT 5190 5189 5191 CONECT 5191 5190 5192 CONECT 5192 5183 5186 5191 CONECT 5193 5166 5168 5172 CONECT 5194 5195 5196 5197 5198 CONECT 5195 5194 CONECT 5196 5194 CONECT 5197 5194 CONECT 5198 5194 CONECT 5199 5200 5201 5202 5203 CONECT 5200 5199 CONECT 5201 5199 CONECT 5202 5199 CONECT 5203 5199 CONECT 5204 5205 5206 5207 5208 CONECT 5205 5204 CONECT 5206 5204 CONECT 5207 5204 CONECT 5208 5204 MASTER 385 0 7 29 17 0 0 6 5300 3 110 48 END