HEADER REPLICATION 29-AUG-25 9Y1H TITLE S180R HUMAN DNA POLYMERASE BETA, TERNARY COMPLEX DA:DUMPNPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 5'-DEOXYRIBOSE-PHOSPHATE LYASE,5'-DRP LYASE,AP LYASE; COMPND 5 EC: 2.7.7.7,4.2.99.-,4.2.99.18; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TEMPLATE STRAND; COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: PRIMER STRAND; COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DOWNSTREAM; COMPND 18 CHAIN: D; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLB; 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; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630 KEYWDS POLYMERASE, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR B.E.ECKENROTH,S.DOUBLIE REVDAT 1 28-JAN-26 9Y1H 0 JRNL AUTH D.L.SAWYER,B.E.ECKENROTH,C.CHAVIRA,K.ALNAJJAR,J.P.HANLEY, JRNL AUTH 2 J.A.DRAGON,S.DOUBLIE,J.B.SWEASY JRNL TITL THE S180R HUMAN GERMLINE VARIANT OF DNA POLYMERASE BETA IS A JRNL TITL 2 LOW FIDELITY ENZYME WITH REDUCED FLEXIBILITY OF THE FINGERS JRNL TITL 3 DOMAIN. JRNL REF BIOCHEMISTRY 2026 JRNL REFN ISSN 0006-2960 JRNL PMID 41524291 JRNL DOI 10.1021/ACS.BIOCHEM.5C00628 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 54511 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 5445 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 26.4800 - 6.0700 0.98 1733 195 0.1479 0.1568 REMARK 3 2 6.0600 - 4.8300 1.00 1771 187 0.1408 0.1964 REMARK 3 3 4.8200 - 4.2200 1.00 1758 200 0.1195 0.1792 REMARK 3 4 4.2200 - 3.8300 1.00 1804 185 0.1111 0.1473 REMARK 3 5 3.8300 - 3.5600 1.00 1765 183 0.1188 0.1650 REMARK 3 6 3.5600 - 3.3500 1.00 1753 173 0.1293 0.1620 REMARK 3 7 3.3500 - 3.1800 1.00 1801 188 0.1334 0.1713 REMARK 3 8 3.1800 - 3.0400 1.00 1744 203 0.1443 0.2050 REMARK 3 9 3.0400 - 2.9300 1.00 1747 196 0.1496 0.2070 REMARK 3 10 2.9300 - 2.8300 1.00 1775 219 0.1498 0.2165 REMARK 3 11 2.8300 - 2.7400 0.98 1701 177 0.1574 0.2130 REMARK 3 12 2.7400 - 2.6600 0.96 1703 188 0.1677 0.2245 REMARK 3 13 2.6600 - 2.5900 0.95 1729 168 0.1592 0.2264 REMARK 3 14 2.5900 - 2.5300 0.94 1627 174 0.1596 0.2444 REMARK 3 15 2.5300 - 2.4700 0.94 1673 190 0.1547 0.1933 REMARK 3 16 2.4700 - 2.4200 0.93 1626 186 0.1612 0.2433 REMARK 3 17 2.4200 - 2.3700 0.93 1639 199 0.1721 0.2032 REMARK 3 18 2.3700 - 2.3200 0.93 1618 203 0.1781 0.2234 REMARK 3 19 2.3200 - 2.2800 0.93 1655 176 0.1813 0.2207 REMARK 3 20 2.2800 - 2.2400 0.91 1576 161 0.1745 0.2218 REMARK 3 21 2.2400 - 2.2100 0.91 1629 189 0.1806 0.2562 REMARK 3 22 2.2100 - 2.1700 0.91 1623 194 0.1831 0.2359 REMARK 3 23 2.1700 - 2.1400 0.91 1569 171 0.1842 0.2327 REMARK 3 24 2.1400 - 2.1100 0.91 1620 202 0.1954 0.2526 REMARK 3 25 2.1100 - 2.0800 0.91 1569 177 0.2032 0.2391 REMARK 3 26 2.0800 - 2.0600 0.91 1634 194 0.2120 0.2771 REMARK 3 27 2.0600 - 2.0300 0.87 1493 165 0.2242 0.2577 REMARK 3 28 2.0300 - 2.0100 0.77 1372 154 0.2506 0.2913 REMARK 3 29 2.0100 - 1.9800 0.71 1235 126 0.2469 0.3054 REMARK 3 30 1.9800 - 1.9600 0.61 1124 122 0.2661 0.3317 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 3464 REMARK 3 ANGLE : 0.843 4811 REMARK 3 CHIRALITY : 0.048 524 REMARK 3 PLANARITY : 0.008 512 REMARK 3 DIHEDRAL : 19.554 1385 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ((CHAIN D AND RESID 1:5) OR (CHAIN T AND RESID 1:6)) REMARK 3 ORIGIN FOR THE GROUP (A): 25.4373 4.1927 -2.6494 REMARK 3 T TENSOR REMARK 3 T11: 0.4361 T22: 0.7050 REMARK 3 T33: 0.5028 T12: -0.0381 REMARK 3 T13: 0.2674 T23: 0.0911 REMARK 3 L TENSOR REMARK 3 L11: 0.9269 L22: 1.8485 REMARK 3 L33: 2.1483 L12: -0.4047 REMARK 3 L13: 0.7375 L23: 1.2943 REMARK 3 S TENSOR REMARK 3 S11: 0.3057 S12: 0.9582 S13: 0.9704 REMARK 3 S21: -1.2881 S22: 0.0342 S23: -1.0059 REMARK 3 S31: -0.4756 S32: 0.8587 S33: -0.0953 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ((CHAIN P AND RESID 6:10) OR (CHAIN T AND RESID REMARK 3 7:11)) REMARK 3 ORIGIN FOR THE GROUP (A): 12.6673 16.2594 14.4670 REMARK 3 T TENSOR REMARK 3 T11: 0.1744 T22: 0.1387 REMARK 3 T33: 0.2146 T12: -0.0606 REMARK 3 T13: 0.0215 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 0.4456 L22: 0.9545 REMARK 3 L33: 0.6029 L12: -0.6485 REMARK 3 L13: -0.1037 L23: 0.0658 REMARK 3 S TENSOR REMARK 3 S11: 0.1106 S12: -0.0592 S13: 0.3252 REMARK 3 S21: -0.0766 S22: -0.0254 S23: -0.5315 REMARK 3 S31: 0.1065 S32: 0.1278 S33: 0.1500 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 12:90 REMARK 3 ORIGIN FOR THE GROUP (A): 22.3959 -8.4363 10.2988 REMARK 3 T TENSOR REMARK 3 T11: 0.1736 T22: 0.2349 REMARK 3 T33: 0.1904 T12: 0.0411 REMARK 3 T13: -0.0047 T23: -0.0576 REMARK 3 L TENSOR REMARK 3 L11: 0.7905 L22: 1.2359 REMARK 3 L33: 0.7936 L12: -0.4006 REMARK 3 L13: 0.7559 L23: -0.0915 REMARK 3 S TENSOR REMARK 3 S11: 0.0230 S12: 0.1159 S13: -0.0419 REMARK 3 S21: -0.0291 S22: 0.0570 S23: -0.2306 REMARK 3 S31: 0.2393 S32: 0.3353 S33: -0.0009 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 91:150 REMARK 3 ORIGIN FOR THE GROUP (A): 17.0426 6.9216 30.2123 REMARK 3 T TENSOR REMARK 3 T11: 0.1708 T22: 0.2655 REMARK 3 T33: 0.1927 T12: -0.0158 REMARK 3 T13: -0.0391 T23: -0.0273 REMARK 3 L TENSOR REMARK 3 L11: 1.0192 L22: 0.6289 REMARK 3 L33: 0.7431 L12: 0.2595 REMARK 3 L13: -0.3602 L23: -0.0134 REMARK 3 S TENSOR REMARK 3 S11: 0.0425 S12: -0.4151 S13: -0.0136 REMARK 3 S21: 0.1384 S22: 0.0095 S23: -0.1904 REMARK 3 S31: 0.0222 S32: 0.3288 S33: -0.0121 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND RESID 151:260 REMARK 3 ORIGIN FOR THE GROUP (A): -6.2444 10.9113 19.9731 REMARK 3 T TENSOR REMARK 3 T11: 0.0914 T22: 0.1617 REMARK 3 T33: 0.1288 T12: -0.0107 REMARK 3 T13: 0.0028 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 1.1483 L22: 1.0397 REMARK 3 L33: 2.3011 L12: -0.0253 REMARK 3 L13: -0.2005 L23: 0.3370 REMARK 3 S TENSOR REMARK 3 S11: -0.0119 S12: -0.0858 S13: 0.0927 REMARK 3 S21: 0.0257 S22: 0.0209 S23: 0.1000 REMARK 3 S31: -0.0210 S32: -0.3411 S33: -0.0072 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND RESID 261:335 REMARK 3 ORIGIN FOR THE GROUP (A): 2.9629 8.5214 -1.7845 REMARK 3 T TENSOR REMARK 3 T11: 0.2095 T22: 0.1539 REMARK 3 T33: 0.1385 T12: -0.0071 REMARK 3 T13: 0.0278 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 1.1456 L22: 0.9599 REMARK 3 L33: 1.3221 L12: -0.0846 REMARK 3 L13: -0.1209 L23: 0.3524 REMARK 3 S TENSOR REMARK 3 S11: 0.0581 S12: 0.2600 S13: 0.0221 REMARK 3 S21: -0.4503 S22: -0.0504 S23: -0.1147 REMARK 3 S31: 0.0154 S32: -0.0449 S33: 0.0065 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ((CHAIN P AND RESID 1:5) OR (CHAIN T AND RESID REMARK 3 12:16)) REMARK 3 ORIGIN FOR THE GROUP (A): 18.8597 30.6350 17.9367 REMARK 3 T TENSOR REMARK 3 T11: 0.3378 T22: 0.2651 REMARK 3 T33: 0.4519 T12: -0.1014 REMARK 3 T13: 0.0192 T23: -0.0446 REMARK 3 L TENSOR REMARK 3 L11: 1.6079 L22: 1.7873 REMARK 3 L33: 1.4017 L12: -1.2725 REMARK 3 L13: -0.4800 L23: -0.6037 REMARK 3 S TENSOR REMARK 3 S11: 0.1346 S12: 0.0353 S13: 0.1355 REMARK 3 S21: -0.5313 S22: -0.6216 S23: -0.6342 REMARK 3 S31: 0.0431 S32: -0.1018 S33: -0.3558 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MODEL REFINEMENT USES I+/I-. DATA REMARK 3 COLLECTION STATISTICS REPORTED FOR I-MEAN SO % COMPLETENESS AND REMARK 3 NUMBER OR REFLECTIONS MAY DIFFER BETWEEN TABLES. REMARK 4 REMARK 4 9Y1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1000299665. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER IMUS MICROFOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS 3 REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS 3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54511 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 26.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.42300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: CRYOPROTECTION WITH 19% PEG 3350, 150 MM SODIUM ACETATE, REMARK 200 50 MM MAGNESIUM CHLORIDE, 50 MM MAGNESIUM ACETATE, 50 MM HEPES, REMARK 200 1 MM TECP, 15% ETHYLENE GLYCOL WITH 1 MM DNTP REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13-16% PEG 3350, 150-300 MM SODIUM REMARK 280 ACETATE, 50 MM HEPES, 1 MM TECP 250UM PROTEIN WITH 300 UM DNA REMARK 280 ASSEMBLY MIXED 1:1 WITH REAGENT, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 39.61200 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 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 LYS A 248 CG CD CE NZ REMARK 470 VAL A 303 CG1 CG2 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 A 546 O HOH A 769 1.94 REMARK 500 O HOH A 688 O HOH A 806 2.03 REMARK 500 O HOH A 752 O HOH P 123 2.08 REMARK 500 O HOH T 105 O HOH P 105 2.09 REMARK 500 O HOH A 790 O HOH T 136 2.12 REMARK 500 O HOH A 694 O HOH A 817 2.15 REMARK 500 O HOH T 104 O HOH T 150 2.17 REMARK 500 O HOH A 624 O HOH A 804 2.17 REMARK 500 O HOH A 520 O HOH A 793 2.18 REMARK 500 OP2 DG P 7 O HOH P 101 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 760 O HOH A 774 1554 2.11 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 DG D 1 P DG D 1 OP3 -0.133 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 DC T 8 O4' - C1' - N1 ANGL. DEV. = 2.1 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 CYS A 178 -152.96 -106.81 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 NA A 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 91.3 REMARK 620 3 VAL A 65 O 90.7 98.8 REMARK 620 4 HOH A 714 O 89.9 78.4 177.1 REMARK 620 5 DC D 3 OP1 174.1 94.5 89.4 90.3 REMARK 620 6 HOH D 105 O 92.8 167.5 93.0 89.8 81.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 VAL A 103 O 95.7 REMARK 620 3 ILE A 106 O 94.5 89.7 REMARK 620 4 HOH A 752 O 83.3 91.5 177.6 REMARK 620 5 DG P 9 OP1 167.2 95.0 92.5 89.4 REMARK 620 6 HOH P 103 O 80.2 176.0 90.6 88.0 89.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 97.0 REMARK 620 3 DUP A 405 O1A 100.3 91.7 REMARK 620 4 DUP A 405 O1B 167.4 89.6 90.2 REMARK 620 5 DUP A 405 O1G 86.4 176.5 88.6 86.9 REMARK 620 6 HOH A 575 O 84.3 86.9 175.3 85.4 92.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD2 REMARK 620 2 ASP A 192 OD1 110.6 REMARK 620 3 ASP A 256 OD2 103.5 100.3 REMARK 620 4 DUP A 405 O1A 91.4 89.5 157.7 REMARK 620 5 HOH A 571 O 78.7 165.7 87.6 79.1 REMARK 620 6 DC P 10 O3' 162.0 85.9 65.0 96.1 86.7 REMARK 620 N 1 2 3 4 5 DBREF 9Y1H A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 9Y1H T 1 16 PDB 9Y1H 9Y1H 1 16 DBREF 9Y1H P 1 10 PDB 9Y1H 9Y1H 1 10 DBREF 9Y1H D 1 5 PDB 9Y1H 9Y1H 1 5 SEQADV 9Y1H ARG A 180 UNP P06746 SER 180 ENGINEERED MUTATION SEQRES 1 A 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY ARG PHE ARG SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU SEQRES 1 T 16 DC DC DG DA DC DA DG DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DC SEQRES 1 D 5 DG DT DC DG DG HET NA A 401 1 HET NA A 402 1 HET MG A 403 1 HET MG A 404 1 HET DUP A 405 28 HET CL A 406 1 HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM CL CHLORIDE ION FORMUL 5 NA 2(NA 1+) FORMUL 7 MG 2(MG 2+) FORMUL 9 DUP C9 H16 N3 O13 P3 FORMUL 10 CL CL 1- FORMUL 11 HOH *416(H2 O) HELIX 1 AA1 ASN A 12 VAL A 29 1 18 HELIX 2 AA2 ALA A 32 LYS A 48 1 17 HELIX 3 AA3 SER A 55 LYS A 61 1 7 HELIX 4 AA4 GLY A 66 GLY A 80 1 15 HELIX 5 AA5 LEU A 82 ASP A 91 1 10 HELIX 6 AA6 ASP A 91 THR A 101 1 11 HELIX 7 AA7 GLY A 107 GLU A 117 1 11 HELIX 8 AA8 THR A 121 ASN A 128 1 8 HELIX 9 AA9 GLU A 129 LEU A 132 5 4 HELIX 10 AB1 ASN A 133 TYR A 142 1 10 HELIX 11 AB2 TYR A 142 GLU A 147 1 6 HELIX 12 AB3 ARG A 152 ASP A 170 1 19 HELIX 13 AB4 CYS A 178 ARG A 183 1 6 HELIX 14 AB5 LYS A 209 VAL A 221 1 13 HELIX 15 AB6 PRO A 261 ASP A 263 5 3 HELIX 16 AB7 GLN A 264 GLY A 274 1 11 HELIX 17 AB8 SER A 275 LYS A 289 1 15 HELIX 18 AB9 SER A 315 ILE A 323 1 9 HELIX 19 AC1 GLU A 329 ARG A 333 5 5 SHEET 1 AA1 2 ILE A 150 PRO A 151 0 SHEET 2 AA1 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 AA2 5 ILE A 174 VAL A 177 0 SHEET 2 AA2 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 AA2 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195 SHEET 4 AA2 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 AA2 5 ILE A 224 LYS A 230 -1 N LEU A 228 O MET A 236 SHEET 1 AA3 2 PHE A 291 ILE A 293 0 SHEET 2 AA3 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O LYS A 60 NA NA A 401 1555 1555 2.39 LINK O LEU A 62 NA NA A 401 1555 1555 2.31 LINK O VAL A 65 NA NA A 401 1555 1555 2.29 LINK O THR A 101 NA NA A 402 1555 1555 2.27 LINK O VAL A 103 NA NA A 402 1555 1555 2.44 LINK O ILE A 106 NA NA A 402 1555 1555 2.40 LINK OD1 ASP A 190 MG MG A 403 1555 1555 1.94 LINK OD2 ASP A 190 MG MG A 404 1555 1555 2.04 LINK OD2 ASP A 192 MG MG A 403 1555 1555 2.07 LINK OD1 ASP A 192 MG MG A 404 1555 1555 2.06 LINK OD2 ASP A 256 MG MG A 404 1555 1555 2.15 LINK NA NA A 401 O HOH A 714 1555 1555 2.62 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.63 LINK NA NA A 401 O HOH D 105 1555 1555 2.78 LINK NA NA A 402 O HOH A 752 1555 1555 2.51 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.35 LINK NA NA A 402 O HOH P 103 1555 1555 2.47 LINK MG MG A 403 O1A DUP A 405 1555 1555 2.11 LINK MG MG A 403 O1B DUP A 405 1555 1555 2.09 LINK MG MG A 403 O1G DUP A 405 1555 1555 2.04 LINK MG MG A 403 O HOH A 575 1555 1555 2.05 LINK MG MG A 404 O1A DUP A 405 1555 1555 2.31 LINK MG MG A 404 O HOH A 571 1555 1555 2.41 LINK MG MG A 404 O3' DC P 10 1555 1555 2.64 CISPEP 1 GLY A 274 SER A 275 0 3.25 CRYST1 50.404 79.224 55.467 90.00 107.29 90.00 P 1 21 1 2 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 0.019840 0.000000 0.006176 0.00000 SCALE2 0.000000 0.012622 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018882 0.00000 CONECT 394 3306 CONECT 412 3306 CONECT 431 3306 CONECT 722 3307 CONECT 740 3307 CONECT 757 3307 CONECT 1461 3308 CONECT 1462 3309 CONECT 1482 3309 CONECT 1483 3308 CONECT 2014 3309 CONECT 3158 3307 CONECT 3187 3309 CONECT 3243 3306 CONECT 3306 394 412 431 3243 CONECT 3306 3552 3748 CONECT 3307 722 740 757 3158 CONECT 3307 3590 3722 CONECT 3308 1461 1483 3327 3331 CONECT 3308 3336 3413 CONECT 3309 1462 1482 2014 3187 CONECT 3309 3327 3409 CONECT 3310 3311 CONECT 3311 3310 3312 3314 CONECT 3312 3311 3313 CONECT 3313 3312 3317 CONECT 3314 3311 3315 CONECT 3315 3314 3316 3317 CONECT 3316 3315 CONECT 3317 3313 3315 3318 CONECT 3318 3317 3319 3322 CONECT 3319 3318 3320 CONECT 3320 3319 3321 3323 CONECT 3321 3320 CONECT 3322 3318 3323 CONECT 3323 3320 3322 3324 CONECT 3324 3323 3325 CONECT 3325 3324 3326 CONECT 3326 3325 3327 3328 3329 CONECT 3327 3308 3309 3326 CONECT 3328 3326 CONECT 3329 3326 3330 CONECT 3330 3329 3331 3332 3333 CONECT 3331 3308 3330 CONECT 3332 3330 CONECT 3333 3330 3334 CONECT 3334 3333 3335 3336 3337 CONECT 3335 3334 CONECT 3336 3308 3334 CONECT 3337 3334 CONECT 3409 3309 CONECT 3413 3308 CONECT 3552 3306 CONECT 3590 3307 CONECT 3722 3307 CONECT 3748 3306 MASTER 492 0 6 19 9 0 0 6 3693 4 56 30 END