HEADER REPLICATION 29-AUG-25 9Y1I TITLE S180R HUMAN DNA POLYMERASE BETA, TERNARY COMPLEX DG:DCMPCPP 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 9Y1I 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. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 43866 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 4362 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 23.7800 - 6.6500 0.97 1300 161 0.1209 0.1379 REMARK 3 2 6.6300 - 5.2800 1.00 1386 138 0.1289 0.1957 REMARK 3 3 5.2800 - 4.6200 1.00 1324 139 0.1326 0.1783 REMARK 3 4 4.6200 - 4.2000 1.00 1350 165 0.1133 0.1544 REMARK 3 5 4.2000 - 3.9000 1.00 1341 131 0.1223 0.1574 REMARK 3 6 3.9000 - 3.6700 1.00 1379 145 0.1277 0.1714 REMARK 3 7 3.6700 - 3.4900 0.99 1359 118 0.1275 0.1784 REMARK 3 8 3.4900 - 3.3400 1.00 1372 159 0.1381 0.2238 REMARK 3 9 3.3400 - 3.2100 1.00 1396 123 0.1447 0.1509 REMARK 3 10 3.2100 - 3.1000 1.00 1336 147 0.1563 0.2272 REMARK 3 11 3.1000 - 3.0000 1.00 1333 174 0.1689 0.2384 REMARK 3 12 3.0000 - 2.9200 1.00 1364 131 0.1677 0.1764 REMARK 3 13 2.9200 - 2.8400 1.00 1327 177 0.1734 0.2501 REMARK 3 14 2.8400 - 2.7700 1.00 1336 155 0.1645 0.2560 REMARK 3 15 2.7700 - 2.7100 1.00 1375 127 0.1851 0.2115 REMARK 3 16 2.7100 - 2.6500 1.00 1353 150 0.1820 0.2794 REMARK 3 17 2.6500 - 2.6000 1.00 1373 133 0.1810 0.3013 REMARK 3 18 2.6000 - 2.5500 1.00 1342 159 0.1742 0.2463 REMARK 3 19 2.5500 - 2.5000 0.98 1337 142 0.1838 0.2362 REMARK 3 20 2.5000 - 2.4600 0.98 1371 155 0.1857 0.2708 REMARK 3 21 2.4600 - 2.4200 0.99 1239 149 0.1900 0.2680 REMARK 3 22 2.4200 - 2.3800 0.99 1395 159 0.1979 0.2696 REMARK 3 23 2.3800 - 2.3500 1.00 1346 149 0.2053 0.2306 REMARK 3 24 2.3500 - 2.3200 1.00 1300 166 0.1822 0.2707 REMARK 3 25 2.3200 - 2.2800 1.00 1407 150 0.2004 0.2553 REMARK 3 26 2.2800 - 2.2600 1.00 1322 145 0.1970 0.2788 REMARK 3 27 2.2500 - 2.2300 0.95 1278 156 0.1994 0.2746 REMARK 3 28 2.2300 - 2.2000 0.88 1150 133 0.2206 0.2732 REMARK 3 29 2.2000 - 2.1700 0.76 1057 121 0.2321 0.2834 REMARK 3 30 2.1700 - 2.1500 0.70 956 105 0.2297 0.2891 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.10 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 : 0.004 3431 REMARK 3 ANGLE : 0.669 4762 REMARK 3 CHIRALITY : 0.042 519 REMARK 3 PLANARITY : 0.006 505 REMARK 3 DIHEDRAL : 19.549 1358 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): 25.2522 4.4356 -2.7136 REMARK 3 T TENSOR REMARK 3 T11: 0.5054 T22: 0.5294 REMARK 3 T33: 0.3848 T12: 0.0614 REMARK 3 T13: 0.1942 T23: 0.1052 REMARK 3 L TENSOR REMARK 3 L11: 0.1006 L22: 0.0241 REMARK 3 L33: 0.2111 L12: -0.0236 REMARK 3 L13: 0.0210 L23: 0.1372 REMARK 3 S TENSOR REMARK 3 S11: 0.4454 S12: 0.4801 S13: 0.7567 REMARK 3 S21: -0.8181 S22: -0.1771 S23: -0.4957 REMARK 3 S31: -0.1083 S32: 0.2419 S33: 0.0094 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): 12.5590 16.3436 14.4084 REMARK 3 T TENSOR REMARK 3 T11: 0.2036 T22: 0.1472 REMARK 3 T33: 0.2129 T12: -0.0355 REMARK 3 T13: 0.0375 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 0.4885 L22: 0.4109 REMARK 3 L33: 0.6242 L12: -0.4162 REMARK 3 L13: 0.2870 L23: -0.0139 REMARK 3 S TENSOR REMARK 3 S11: 0.0842 S12: -0.0232 S13: 0.3510 REMARK 3 S21: -0.1874 S22: -0.1184 S23: -0.4599 REMARK 3 S31: -0.0618 S32: 0.1548 S33: -0.0215 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 12:90 REMARK 3 ORIGIN FOR THE GROUP (A): 22.2984 -8.5615 10.1490 REMARK 3 T TENSOR REMARK 3 T11: 0.1975 T22: 0.2083 REMARK 3 T33: 0.1556 T12: 0.0493 REMARK 3 T13: 0.0053 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 1.3961 L22: 2.5429 REMARK 3 L33: 1.2356 L12: -0.1444 REMARK 3 L13: -0.2062 L23: 0.4760 REMARK 3 S TENSOR REMARK 3 S11: 0.0642 S12: 0.0491 S13: 0.0011 REMARK 3 S21: -0.2341 S22: 0.0317 S23: -0.1919 REMARK 3 S31: 0.0972 S32: 0.2891 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 91:150 REMARK 3 ORIGIN FOR THE GROUP (A): 17.3310 7.3403 30.3300 REMARK 3 T TENSOR REMARK 3 T11: 0.1293 T22: 0.2200 REMARK 3 T33: 0.1850 T12: -0.0082 REMARK 3 T13: -0.0401 T23: -0.0213 REMARK 3 L TENSOR REMARK 3 L11: 1.4375 L22: 1.0681 REMARK 3 L33: 1.6260 L12: 0.2434 REMARK 3 L13: -0.6248 L23: -0.3367 REMARK 3 S TENSOR REMARK 3 S11: 0.0997 S12: -0.2485 S13: -0.0879 REMARK 3 S21: 0.1360 S22: -0.0438 S23: -0.2233 REMARK 3 S31: -0.1129 S32: 0.3352 S33: -0.0034 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND RESID 151:260 REMARK 3 ORIGIN FOR THE GROUP (A): -6.3052 10.7157 20.1657 REMARK 3 T TENSOR REMARK 3 T11: 0.0802 T22: 0.1913 REMARK 3 T33: 0.1704 T12: 0.0269 REMARK 3 T13: 0.0139 T23: 0.0059 REMARK 3 L TENSOR REMARK 3 L11: 1.3159 L22: 1.7721 REMARK 3 L33: 2.5776 L12: 0.3163 REMARK 3 L13: 0.1444 L23: -0.1240 REMARK 3 S TENSOR REMARK 3 S11: 0.0112 S12: -0.0754 S13: 0.0115 REMARK 3 S21: -0.0215 S22: 0.0263 S23: 0.2083 REMARK 3 S31: -0.1126 S32: -0.3953 S33: 0.0049 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND RESID 261:335 REMARK 3 ORIGIN FOR THE GROUP (A): 3.0769 8.6408 -1.8606 REMARK 3 T TENSOR REMARK 3 T11: 0.2929 T22: 0.1919 REMARK 3 T33: 0.1764 T12: -0.0177 REMARK 3 T13: -0.0080 T23: -0.0130 REMARK 3 L TENSOR REMARK 3 L11: 1.2918 L22: 1.8238 REMARK 3 L33: 1.8962 L12: -0.3228 REMARK 3 L13: -0.3122 L23: 0.3894 REMARK 3 S TENSOR REMARK 3 S11: -0.0371 S12: 0.2350 S13: 0.0286 REMARK 3 S21: -0.6258 S22: 0.0369 S23: -0.1115 REMARK 3 S31: -0.0551 S32: -0.0050 S33: -0.0004 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): 18.8189 30.8574 17.8802 REMARK 3 T TENSOR REMARK 3 T11: 0.3182 T22: 0.2134 REMARK 3 T33: 0.5727 T12: -0.0687 REMARK 3 T13: 0.0235 T23: -0.0517 REMARK 3 L TENSOR REMARK 3 L11: 0.5462 L22: 2.5750 REMARK 3 L33: 2.1654 L12: -0.3696 REMARK 3 L13: 0.6024 L23: -1.6305 REMARK 3 S TENSOR REMARK 3 S11: 0.0175 S12: -0.2363 S13: 0.3401 REMARK 3 S21: -0.5684 S22: -0.5778 S23: -0.7018 REMARK 3 S31: 0.2127 S32: -0.2232 S33: -0.4031 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 9Y1I 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_1000299669. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-23 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 : 43866 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 24.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.860 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.72 REMARK 200 R MERGE FOR SHELL (I) : 0.29900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 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 (%): 45.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 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 39.94350 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: 5230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 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 512 O HOH A 693 2.08 REMARK 500 O HOH A 793 O HOH T 111 2.18 REMARK 500 O HOH A 706 O HOH A 773 2.19 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 -0.123 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 -153.37 -121.47 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 90.8 REMARK 620 3 VAL A 65 O 94.9 105.6 REMARK 620 4 HOH A 686 O 87.7 73.6 177.4 REMARK 620 5 DC D 3 OP1 169.4 98.7 87.0 90.6 REMARK 620 N 1 2 3 4 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 95.2 REMARK 620 3 ILE A 106 O 89.9 86.2 REMARK 620 4 HOH A 749 O 85.7 90.9 174.4 REMARK 620 5 DG P 9 OP1 166.3 97.5 96.2 88.9 REMARK 620 6 HOH P 109 O 78.3 171.0 87.5 94.8 89.7 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 96.5 REMARK 620 3 XC5 A 405 O1A 95.1 85.3 REMARK 620 4 XC5 A 405 O2B 174.0 88.0 89.2 REMARK 620 5 XC5 A 405 O3G 85.4 175.4 90.4 90.5 REMARK 620 6 HOH A 602 O 85.0 92.8 178.1 90.9 91.6 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 98.4 REMARK 620 3 ASP A 256 OD2 86.9 92.7 REMARK 620 4 XC5 A 405 O1A 95.8 92.2 174.0 REMARK 620 5 HOH A 518 O 86.5 174.0 90.9 83.9 REMARK 620 6 DC P 10 O3' 167.2 89.7 82.8 93.7 86.1 REMARK 620 N 1 2 3 4 5 DBREF 9Y1I A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 9Y1I T 1 16 PDB 9Y1I 9Y1I 1 16 DBREF 9Y1I P 1 10 PDB 9Y1I 9Y1I 1 10 DBREF 9Y1I D 1 5 PDB 9Y1I 9Y1I 1 5 SEQADV 9Y1I 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 DG 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 XC5 A 405 28 HET CL A 406 1 HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETNAM XC5 2'-DEOXY-5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 2 XC5 PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE HETNAM CL CHLORIDE ION FORMUL 5 NA 2(NA 1+) FORMUL 7 MG 2(MG 2+) FORMUL 9 XC5 C10 H18 N3 O12 P3 FORMUL 10 CL CL 1- FORMUL 11 HOH *384(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 ASP A 256 N VAL A 193 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 2.43 LINK O LEU A 62 NA NA A 401 1555 1555 2.24 LINK O VAL A 65 NA NA A 401 1555 1555 2.22 LINK O THR A 101 NA NA A 402 1555 1555 2.34 LINK O VAL A 103 NA NA A 402 1555 1555 2.50 LINK O ILE A 106 NA NA A 402 1555 1555 2.43 LINK OD1 ASP A 190 MG MG A 403 1555 1555 1.98 LINK OD2 ASP A 190 MG MG A 404 1555 1555 2.06 LINK OD2 ASP A 192 MG MG A 403 1555 1555 2.13 LINK OD1 ASP A 192 MG MG A 404 1555 1555 2.02 LINK OD2 ASP A 256 MG MG A 404 1555 1555 2.05 LINK NA NA A 401 O HOH A 686 1555 1555 2.67 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.53 LINK NA NA A 402 O HOH A 749 1555 1555 2.74 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.46 LINK NA NA A 402 O HOH P 109 1555 1555 2.38 LINK MG MG A 403 O1A XC5 A 405 1555 1555 2.11 LINK MG MG A 403 O2B XC5 A 405 1555 1555 2.04 LINK MG MG A 403 O3G XC5 A 405 1555 1555 2.11 LINK MG MG A 403 O HOH A 602 1555 1555 2.11 LINK MG MG A 404 O1A XC5 A 405 1555 1555 2.22 LINK MG MG A 404 O HOH A 518 1555 1555 2.02 LINK MG MG A 404 O3' DC P 10 1555 1555 2.16 CISPEP 1 GLY A 274 SER A 275 0 -0.46 CRYST1 50.776 79.887 55.359 90.00 107.52 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 0.019694 0.000000 0.006217 0.00000 SCALE2 0.000000 0.012518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018943 0.00000 CONECT 388 3278 CONECT 406 3278 CONECT 425 3278 CONECT 716 3279 CONECT 734 3279 CONECT 751 3279 CONECT 1457 3280 CONECT 1458 3281 CONECT 1473 3281 CONECT 1474 3280 CONECT 1991 3281 CONECT 3130 3279 CONECT 3159 3281 CONECT 3215 3278 CONECT 3278 388 406 425 3215 CONECT 3278 3496 CONECT 3279 716 734 751 3130 CONECT 3279 3559 3663 CONECT 3280 1457 1474 3283 3288 CONECT 3280 3293 3412 CONECT 3281 1458 1473 1991 3159 CONECT 3281 3283 3328 CONECT 3282 3283 3284 3285 3307 CONECT 3283 3280 3281 3282 CONECT 3284 3282 CONECT 3285 3282 3286 CONECT 3286 3285 3287 3288 3289 CONECT 3287 3286 CONECT 3288 3280 3286 CONECT 3289 3286 3290 CONECT 3290 3289 3291 3292 3293 CONECT 3291 3290 CONECT 3292 3290 CONECT 3293 3280 3290 CONECT 3294 3295 3299 3302 CONECT 3295 3294 3296 3300 CONECT 3296 3295 3297 CONECT 3297 3296 3298 3301 CONECT 3298 3297 3299 CONECT 3299 3294 3298 CONECT 3300 3295 CONECT 3301 3297 CONECT 3302 3294 3303 3306 CONECT 3303 3302 3304 CONECT 3304 3303 3305 3309 CONECT 3305 3304 3306 3308 CONECT 3306 3302 3305 CONECT 3307 3282 3308 CONECT 3308 3305 3307 CONECT 3309 3304 CONECT 3328 3281 CONECT 3412 3280 CONECT 3496 3278 CONECT 3559 3279 CONECT 3663 3279 MASTER 446 0 6 19 9 0 0 6 3662 4 55 30 END