HEADER REPLICATION/DNA 03-MAR-23 8ILE TITLE THE CRYSTAL STRUCTURE OF DGTPALPHASE-RP:DNAPRE-II:POL X SUBSTRATE TITLE 2 TERNARY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPAIR DNA POLYMERASE X; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: POL X,ASFVPOLX; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*TP*GP*GP*AP*TP*CP*CP*A)-3'); COMPND 9 CHAIN: E, G; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AFRICAN SWINE FEVER VIRUS (STRAIN BADAJOZ 1971 SOURCE 3 VERO-ADAPTED); SOURCE 4 ORGANISM_TAXID: 10498; SOURCE 5 GENE: BA71V-97, O174L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE, SUBSTRATE COMPLEX, SELENIUM-MODIFIED DNTP, KEYWDS 2 CONFIGURATION, REPLICATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.QIN,J.H.GAN,Z.HUANG REVDAT 1 10-JAN-24 8ILE 0 JRNL AUTH T.QIN,B.HU,Q.ZHAO,Y.WANG,S.WANG,D.LUO,J.LYU,Y.CHEN,J.GAN, JRNL AUTH 2 Z.HUANG JRNL TITL STRUCTURAL INSIGHT INTO POLYMERASE MECHANISM VIA A CHIRAL JRNL TITL 2 CENTER GENERATED WITH A SINGLE SELENIUM ATOM. JRNL REF INT J MOL SCI V. 24 2023 JRNL REFN ESSN 1422-0067 JRNL PMID 37958741 JRNL DOI 10.3390/IJMS242115758 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 9335 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 515 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 408 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 55.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 23 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2650 REMARK 3 NUCLEIC ACID ATOMS : 358 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -23.49000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : 23.61000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.323 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 38.321 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.912 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.857 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3163 ; 0.009 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 2893 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4374 ; 1.416 ; 1.893 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6603 ; 1.076 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 343 ; 6.086 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 99 ;32.830 ;23.131 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 467 ;16.056 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;16.686 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 503 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3217 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 690 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): 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): 1381 ; 3.251 ; 3.731 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1380 ; 3.251 ; 3.730 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1721 ; 4.589 ; 5.587 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1722 ; 4.587 ; 5.588 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1782 ; 3.330 ; 3.490 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1779 ; 3.329 ; 3.486 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2652 ; 4.459 ; 5.194 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3480 ; 6.033 ;28.691 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3479 ; 6.017 ;28.692 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6056 ; 3.058 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 1 ;70.625 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5970 ;12.954 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A B 18582 0.07 0.05 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 1 A 174 REMARK 3 ORIGIN FOR THE GROUP (A): 15.1779 -23.0868 -35.3955 REMARK 3 T TENSOR REMARK 3 T11: 0.4541 T22: 0.1482 REMARK 3 T33: 0.0594 T12: -0.0677 REMARK 3 T13: 0.0736 T23: 0.0065 REMARK 3 L TENSOR REMARK 3 L11: 6.3339 L22: 2.6341 REMARK 3 L33: 4.9742 L12: 0.3264 REMARK 3 L13: -1.7003 L23: 0.2144 REMARK 3 S TENSOR REMARK 3 S11: -0.0970 S12: 0.3769 S13: -0.4594 REMARK 3 S21: -0.6808 S22: -0.1995 S23: -0.2150 REMARK 3 S31: 0.5660 S32: -0.0277 S33: 0.2965 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 1 B 174 REMARK 3 ORIGIN FOR THE GROUP (A): -11.8307 -22.1505 -4.6275 REMARK 3 T TENSOR REMARK 3 T11: 0.0352 T22: 0.0510 REMARK 3 T33: 0.0723 T12: 0.0289 REMARK 3 T13: -0.0013 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 3.7619 L22: 3.4762 REMARK 3 L33: 3.1106 L12: 0.8519 REMARK 3 L13: 1.3315 L23: 1.7115 REMARK 3 S TENSOR REMARK 3 S11: -0.1900 S12: -0.3591 S13: 0.0248 REMARK 3 S21: -0.0460 S22: -0.1640 S23: 0.3934 REMARK 3 S31: -0.2119 S32: -0.1177 S33: 0.3540 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 : E 0 E 8 REMARK 3 ORIGIN FOR THE GROUP (A): 1.3854 -20.6081 -17.7467 REMARK 3 T TENSOR REMARK 3 T11: 0.3688 T22: 0.2242 REMARK 3 T33: 0.1190 T12: -0.0848 REMARK 3 T13: 0.0292 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 6.6694 L22: 0.1236 REMARK 3 L33: 3.8350 L12: -0.9069 REMARK 3 L13: -5.0299 L23: 0.6840 REMARK 3 S TENSOR REMARK 3 S11: 0.2040 S12: 0.1720 S13: 0.1765 REMARK 3 S21: -0.0310 S22: -0.0391 S23: -0.0206 REMARK 3 S31: -0.2829 S32: -0.0948 S33: -0.1649 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 : G 2 G 10 REMARK 3 ORIGIN FOR THE GROUP (A): 3.9596 -21.2511 -20.2356 REMARK 3 T TENSOR REMARK 3 T11: 0.1715 T22: 0.2526 REMARK 3 T33: 0.1315 T12: -0.1143 REMARK 3 T13: -0.0089 T23: 0.0499 REMARK 3 L TENSOR REMARK 3 L11: 5.9399 L22: 0.3985 REMARK 3 L33: 7.0100 L12: 1.3369 REMARK 3 L13: -4.8527 L23: -1.4574 REMARK 3 S TENSOR REMARK 3 S11: -0.2473 S12: 0.1165 S13: 0.1929 REMARK 3 S21: -0.0697 S22: 0.1500 S23: 0.0321 REMARK 3 S31: -0.1617 S32: -0.0723 S33: 0.0972 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8ILE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 08-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1300035820. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-16 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10889 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.80 REMARK 200 R MERGE FOR SHELL (I) : 1.22500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M L-PROLINE, HEPES PH 8.6 (0.1 REMARK 280 M),10% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 29.74050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.67650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.69100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.67650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.74050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.69100 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E, 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 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 GLY A 0 REMARK 465 TYR A 22 REMARK 465 ASN A 23 REMARK 465 GLY A 24 REMARK 465 GLN A 25 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 5 CD1 REMARK 470 LYS A 9 CD CE NZ REMARK 470 GLU A 21 CG CD OE1 OE2 REMARK 470 LEU A 26 CG CD1 CD2 REMARK 470 LYS A 28 CG CD CE NZ REMARK 470 LEU A 30 CG CD1 CD2 REMARK 470 LYS A 32 CG CD CE NZ REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 LYS A 59 CG CD CE NZ REMARK 470 LYS A 60 CG CD CE NZ REMARK 470 LYS A 63 CG CD CE NZ REMARK 470 ARG A 70 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 74 CG CD1 CD2 REMARK 470 LYS A 79 CE NZ REMARK 470 GLU A 91 CG CD OE1 OE2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 LYS A 95 CG CD CE NZ REMARK 470 THR A 96 OG1 CG2 REMARK 470 LEU A 105 CG CD1 CD2 REMARK 470 LYS A 109 CG CD CE NZ REMARK 470 ARG A 127 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 130 CG CD1 CD2 REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 LYS A 133 CD CE NZ REMARK 470 TYR A 135 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 144 CG CD CE NZ REMARK 470 ASN A 145 CG OD1 ND2 REMARK 470 GLN A 146 CG CD OE1 NE2 REMARK 470 LYS A 152 CG CD CE NZ REMARK 470 LYS A 161 CG CD CE NZ REMARK 470 LEU A 163 CG CD1 CD2 REMARK 470 PHE A 165 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 167 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 171 CG CD CE NZ REMARK 470 LYS A 172 CG CD CE NZ REMARK 470 LEU B 4 CG CD1 CD2 REMARK 470 ILE B 5 CD1 REMARK 470 LYS B 9 CD CE NZ REMARK 470 ARG B 17 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 28 CG CD CE NZ REMARK 470 LYS B 45 CG CD CE NZ REMARK 470 LYS B 59 CG CD CE NZ REMARK 470 LYS B 63 CG CD CE NZ REMARK 470 LYS B 72 CG CD CE NZ REMARK 470 LYS B 79 CE NZ REMARK 470 GLU B 91 CG CD OE1 OE2 REMARK 470 LYS B 94 CG CD CE NZ REMARK 470 LYS B 95 CE NZ REMARK 470 LYS B 133 CD CE NZ REMARK 470 LYS B 144 NZ REMARK 470 LYS B 152 CG CD CE NZ REMARK 470 DA E 8 O3' REMARK 470 DA G 10 O3' 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 DT E 1 C1' - O4' - C4' ANGL. DEV. = -6.0 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 65 -70.65 -67.52 REMARK 500 ASN A 138 -168.87 -164.63 REMARK 500 VAL B 65 -70.69 -67.13 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 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 49 OD1 REMARK 620 2 ASP A 51 OD2 94.9 REMARK 620 3 7Q6 A 203 O2B 167.4 97.5 REMARK 620 4 7Q6 A 203 SEA 90.3 98.6 85.5 REMARK 620 5 7Q6 A 203 O1G 83.0 176.0 84.7 84.8 REMARK 620 6 HOH A 301 O 91.5 81.9 92.6 178.0 94.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 49 OD2 REMARK 620 2 ASP A 51 OD1 98.7 REMARK 620 3 ASP A 100 OD2 80.0 102.7 REMARK 620 4 7Q6 A 203 SEA 101.7 83.2 173.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 49 OD1 REMARK 620 2 ASP B 51 OD2 97.4 REMARK 620 3 7Q6 B 203 SEA 92.2 112.0 REMARK 620 4 7Q6 B 203 O1G 75.3 164.2 82.6 REMARK 620 5 7Q6 B 203 O2B 165.2 94.7 91.2 90.9 REMARK 620 6 HOH B 301 O 82.2 79.6 167.8 85.5 91.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 49 OD2 REMARK 620 2 ASP B 51 OD1 114.6 REMARK 620 3 ASP B 100 OD2 86.4 116.0 REMARK 620 4 7Q6 B 203 SEA 98.0 97.3 141.1 REMARK 620 N 1 2 3 DBREF 8ILE A 1 174 UNP P42494 DPOLX_ASFB7 1 174 DBREF 8ILE B 1 174 UNP P42494 DPOLX_ASFB7 1 174 DBREF 8ILE E 0 8 PDB 8ILE 8ILE 0 8 DBREF 8ILE G 2 10 PDB 8ILE 8ILE 2 10 SEQADV 8ILE GLY A -1 UNP P42494 EXPRESSION TAG SEQADV 8ILE GLY A 0 UNP P42494 EXPRESSION TAG SEQADV 8ILE GLY B -1 UNP P42494 EXPRESSION TAG SEQADV 8ILE GLY B 0 UNP P42494 EXPRESSION TAG SEQRES 1 A 176 GLY GLY MET LEU THR LEU ILE GLN GLY LYS LYS ILE VAL SEQRES 2 A 176 ASN HIS LEU ARG SER ARG LEU ALA PHE GLU TYR ASN GLY SEQRES 3 A 176 GLN LEU ILE LYS ILE LEU SER LYS ASN ILE VAL ALA VAL SEQRES 4 A 176 GLY SER LEU ARG ARG GLU GLU LYS MET LEU ASN ASP VAL SEQRES 5 A 176 ASP LEU LEU ILE ILE VAL PRO GLU LYS LYS LEU LEU LYS SEQRES 6 A 176 HIS VAL LEU PRO ASN ILE ARG ILE LYS GLY LEU SER PHE SEQRES 7 A 176 SER VAL LYS VAL CYS GLY GLU ARG LYS CYS VAL LEU PHE SEQRES 8 A 176 ILE GLU TRP GLU LYS LYS THR TYR GLN LEU ASP LEU PHE SEQRES 9 A 176 THR ALA LEU ALA GLU GLU LYS PRO TYR ALA ILE PHE HIS SEQRES 10 A 176 PHE THR GLY PRO VAL SER TYR LEU ILE ARG ILE ARG ALA SEQRES 11 A 176 ALA LEU LYS LYS LYS ASN TYR LYS LEU ASN GLN TYR GLY SEQRES 12 A 176 LEU PHE LYS ASN GLN THR LEU VAL PRO LEU LYS ILE THR SEQRES 13 A 176 THR GLU LYS GLU LEU ILE LYS GLU LEU GLY PHE THR TYR SEQRES 14 A 176 ARG ILE PRO LYS LYS ARG LEU SEQRES 1 B 176 GLY GLY MET LEU THR LEU ILE GLN GLY LYS LYS ILE VAL SEQRES 2 B 176 ASN HIS LEU ARG SER ARG LEU ALA PHE GLU TYR ASN GLY SEQRES 3 B 176 GLN LEU ILE LYS ILE LEU SER LYS ASN ILE VAL ALA VAL SEQRES 4 B 176 GLY SER LEU ARG ARG GLU GLU LYS MET LEU ASN ASP VAL SEQRES 5 B 176 ASP LEU LEU ILE ILE VAL PRO GLU LYS LYS LEU LEU LYS SEQRES 6 B 176 HIS VAL LEU PRO ASN ILE ARG ILE LYS GLY LEU SER PHE SEQRES 7 B 176 SER VAL LYS VAL CYS GLY GLU ARG LYS CYS VAL LEU PHE SEQRES 8 B 176 ILE GLU TRP GLU LYS LYS THR TYR GLN LEU ASP LEU PHE SEQRES 9 B 176 THR ALA LEU ALA GLU GLU LYS PRO TYR ALA ILE PHE HIS SEQRES 10 B 176 PHE THR GLY PRO VAL SER TYR LEU ILE ARG ILE ARG ALA SEQRES 11 B 176 ALA LEU LYS LYS LYS ASN TYR LYS LEU ASN GLN TYR GLY SEQRES 12 B 176 LEU PHE LYS ASN GLN THR LEU VAL PRO LEU LYS ILE THR SEQRES 13 B 176 THR GLU LYS GLU LEU ILE LYS GLU LEU GLY PHE THR TYR SEQRES 14 B 176 ARG ILE PRO LYS LYS ARG LEU SEQRES 1 E 9 DC DT DG DG DA DT DC DC DA SEQRES 1 G 9 DC DT DG DG DA DT DC DC DA HET MN A 201 1 HET MN A 202 1 HET 7Q6 A 203 31 HET MN B 201 1 HET MN B 202 1 HET 7Q6 B 203 31 HETNAM MN MANGANESE (II) ION HETNAM 7Q6 [[(2R,3S,5R)-5-(2-AZANYL-6-OXIDANYLIDENE-1H-PURIN-9- HETNAM 2 7Q6 YL)-3-OXIDANYL-OXOLAN-2-YL]METHOXY-SELANYL-PHOSPHORYL] HETNAM 3 7Q6 PHOSPHONO HYDROGEN PHOSPHATE FORMUL 5 MN 4(MN 2+) FORMUL 7 7Q6 2(C10 H16 N5 O12 P3 SE) FORMUL 11 HOH *4(H2 O) HELIX 1 AA1 LEU A 4 ARG A 17 1 14 HELIX 2 AA2 LEU A 30 LYS A 32 5 3 HELIX 3 AA3 VAL A 37 ARG A 42 1 6 HELIX 4 AA4 GLU A 58 HIS A 64 5 7 HELIX 5 AA5 GLU A 108 GLY A 118 1 11 HELIX 6 AA6 PRO A 119 LYS A 132 1 14 HELIX 7 AA7 THR A 155 GLY A 164 1 10 HELIX 8 AA8 ILE A 169 ARG A 173 5 5 HELIX 9 AA9 LEU B 4 SER B 16 1 13 HELIX 10 AB1 LEU B 30 LYS B 32 5 3 HELIX 11 AB2 VAL B 37 ARG B 42 1 6 HELIX 12 AB3 LYS B 60 HIS B 64 5 5 HELIX 13 AB4 GLU B 108 GLY B 118 1 11 HELIX 14 AB5 PRO B 119 LYS B 132 1 14 HELIX 15 AB6 THR B 155 GLY B 164 1 10 HELIX 16 AB7 ILE B 169 ARG B 173 5 5 SHEET 1 AA1 2 LEU A 2 THR A 3 0 SHEET 2 AA1 2 MET A 46 LEU A 47 -1 O LEU A 47 N LEU A 2 SHEET 1 AA2 3 ILE A 27 LYS A 28 0 SHEET 2 AA2 3 LEU A 18 PHE A 20 -1 N PHE A 20 O ILE A 27 SHEET 3 AA2 3 ILE A 69 ILE A 71 -1 O ARG A 70 N ALA A 19 SHEET 1 AA3 5 ILE A 34 ALA A 36 0 SHEET 2 AA3 5 ASP A 49 VAL A 56 -1 O LEU A 53 N VAL A 35 SHEET 3 AA3 5 THR A 96 LEU A 105 1 O ASP A 100 N LEU A 52 SHEET 4 AA3 5 LYS A 85 GLU A 91 -1 N CYS A 86 O LEU A 101 SHEET 5 AA3 5 SER A 75 CYS A 81 -1 N SER A 77 O PHE A 89 SHEET 1 AA4 2 TYR A 135 LEU A 137 0 SHEET 2 AA4 2 LEU A 142 LYS A 144 -1 O PHE A 143 N LYS A 136 SHEET 1 AA5 2 LEU B 2 THR B 3 0 SHEET 2 AA5 2 MET B 46 LEU B 47 -1 O LEU B 47 N LEU B 2 SHEET 1 AA6 3 LEU B 26 LYS B 28 0 SHEET 2 AA6 3 LEU B 18 GLU B 21 -1 N PHE B 20 O ILE B 27 SHEET 3 AA6 3 ILE B 69 ILE B 71 -1 O ARG B 70 N ALA B 19 SHEET 1 AA7 5 ILE B 34 ALA B 36 0 SHEET 2 AA7 5 ASP B 49 VAL B 56 -1 O LEU B 53 N VAL B 35 SHEET 3 AA7 5 THR B 96 LEU B 105 1 O ASP B 100 N LEU B 52 SHEET 4 AA7 5 LYS B 85 GLU B 91 -1 N CYS B 86 O LEU B 101 SHEET 5 AA7 5 SER B 75 CYS B 81 -1 N SER B 77 O PHE B 89 SHEET 1 AA8 2 TYR B 135 LEU B 137 0 SHEET 2 AA8 2 LEU B 142 LYS B 144 -1 O PHE B 143 N LYS B 136 SSBOND 1 CYS A 81 CYS A 86 1555 1555 2.20 SSBOND 2 CYS B 81 CYS B 86 1555 1555 2.07 LINK OD1 ASP A 49 MN MN A 201 1555 1555 2.10 LINK OD2 ASP A 49 MN MN A 202 1555 1555 2.11 LINK OD2 ASP A 51 MN MN A 201 1555 1555 1.98 LINK OD1 ASP A 51 MN MN A 202 1555 1555 2.39 LINK OD2 ASP A 100 MN MN A 202 1555 1555 2.14 LINK MN MN A 201 O2B 7Q6 A 203 1555 1555 2.24 LINK MN MN A 201 SEA 7Q6 A 203 1555 1555 2.54 LINK MN MN A 201 O1G 7Q6 A 203 1555 1555 2.03 LINK MN MN A 201 O HOH A 301 1555 1555 2.01 LINK MN MN A 202 SEA 7Q6 A 203 1555 1555 2.27 LINK OD1 ASP B 49 MN MN B 201 1555 1555 2.13 LINK OD2 ASP B 49 MN MN B 202 1555 1555 2.09 LINK OD2 ASP B 51 MN MN B 201 1555 1555 1.91 LINK OD1 ASP B 51 MN MN B 202 1555 1555 2.13 LINK OD2 ASP B 100 MN MN B 202 1555 1555 2.05 LINK MN MN B 201 SEA 7Q6 B 203 1555 1555 2.86 LINK MN MN B 201 O1G 7Q6 B 203 1555 1555 2.01 LINK MN MN B 201 O2B 7Q6 B 203 1555 1555 2.21 LINK MN MN B 201 O HOH B 301 1555 1555 2.02 LINK MN MN B 202 SEA 7Q6 B 203 1555 1555 2.28 CISPEP 1 GLY A 118 PRO A 119 0 -5.59 CISPEP 2 GLY B 118 PRO B 119 0 -5.55 CRYST1 59.481 77.382 111.353 90.00 90.00 90.00 P 21 21 21 8 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 0.016812 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012923 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008980 0.00000