HEADER REPLICATION 29-AUG-25 9Y1D TITLE S180R HUMAN DNA POLYMERASE BETA, BINARY COMPLEX TEMPLATING DA 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: 2853804; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 2853804; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 2853804 KEYWDS POLYMERASE, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR B.E.ECKENROTH,S.DOUBLIE REVDAT 1 28-JAN-26 9Y1D 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 91118 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.080 REMARK 3 FREE R VALUE TEST SET COUNT : 9189 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 43.6600 - 5.2800 0.94 2771 298 0.1371 0.1520 REMARK 3 2 5.2800 - 4.1900 0.94 2679 320 0.1241 0.1521 REMARK 3 3 4.1900 - 3.6600 0.95 2811 280 0.1196 0.1514 REMARK 3 4 3.6600 - 3.3300 0.94 2786 291 0.1318 0.1611 REMARK 3 5 3.3300 - 3.0900 0.95 2741 338 0.1456 0.1777 REMARK 3 6 3.0900 - 2.9100 0.95 2702 325 0.1611 0.1956 REMARK 3 7 2.9100 - 2.7600 0.95 2758 332 0.1654 0.1906 REMARK 3 8 2.7600 - 2.6400 0.94 2690 330 0.1628 0.2341 REMARK 3 9 2.6400 - 2.5400 0.94 2718 298 0.1650 0.2089 REMARK 3 10 2.5400 - 2.4500 0.94 2764 288 0.1651 0.2241 REMARK 3 11 2.4500 - 2.3800 0.94 2779 265 0.1632 0.2021 REMARK 3 12 2.3800 - 2.3100 0.92 2658 321 0.1588 0.1956 REMARK 3 13 2.3100 - 2.2500 0.93 2674 339 0.1553 0.2001 REMARK 3 14 2.2500 - 2.1900 0.93 2711 290 0.1620 0.2170 REMARK 3 15 2.1900 - 2.1400 0.94 2728 292 0.1862 0.2092 REMARK 3 16 2.1400 - 2.1000 0.93 2700 325 0.1874 0.2270 REMARK 3 17 2.1000 - 2.0500 0.94 2744 288 0.1832 0.2346 REMARK 3 18 2.0500 - 2.0200 0.93 2719 296 0.1751 0.2264 REMARK 3 19 2.0200 - 1.9800 0.94 2732 332 0.1755 0.1969 REMARK 3 20 1.9800 - 1.9500 0.94 2701 316 0.1698 0.2026 REMARK 3 21 1.9500 - 1.9100 0.94 2831 261 0.1756 0.2115 REMARK 3 22 1.9100 - 1.8900 0.95 2702 301 0.1788 0.2375 REMARK 3 23 1.8900 - 1.8600 0.94 2768 359 0.1867 0.2296 REMARK 3 24 1.8600 - 1.8300 0.94 2664 307 0.2015 0.2428 REMARK 3 25 1.8300 - 1.8100 0.95 2762 327 0.2060 0.2408 REMARK 3 26 1.8100 - 1.7800 0.95 2792 256 0.2156 0.2501 REMARK 3 27 1.7800 - 1.7600 0.94 2743 338 0.2436 0.2903 REMARK 3 28 1.7600 - 1.7400 0.94 2711 337 0.2627 0.3062 REMARK 3 29 1.7400 - 1.7200 0.93 2727 267 0.2869 0.3189 REMARK 3 30 1.7200 - 1.7000 0.90 2663 272 0.3060 0.3554 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.20 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 : 0.011 3402 REMARK 3 ANGLE : 1.224 4726 REMARK 3 CHIRALITY : 0.072 524 REMARK 3 PLANARITY : 0.012 499 REMARK 3 DIHEDRAL : 19.909 1344 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): 30.4903 9.7473 -2.7206 REMARK 3 T TENSOR REMARK 3 T11: 0.2493 T22: 0.1833 REMARK 3 T33: 0.1336 T12: 0.0271 REMARK 3 T13: 0.0084 T23: 0.0195 REMARK 3 L TENSOR REMARK 3 L11: 2.6865 L22: 2.7044 REMARK 3 L33: 2.9722 L12: -0.6753 REMARK 3 L13: -0.5709 L23: 0.2783 REMARK 3 S TENSOR REMARK 3 S11: 0.1747 S12: 0.3878 S13: 0.1947 REMARK 3 S21: -0.2470 S22: -0.0839 S23: -0.0267 REMARK 3 S31: 0.1422 S32: 0.1114 S33: -0.0906 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): 15.0023 17.3973 13.9573 REMARK 3 T TENSOR REMARK 3 T11: 0.1696 T22: 0.1521 REMARK 3 T33: 0.1640 T12: -0.0017 REMARK 3 T13: 0.0267 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 1.8769 L22: 3.0301 REMARK 3 L33: 1.9043 L12: -0.1544 REMARK 3 L13: 0.2844 L23: 0.0346 REMARK 3 S TENSOR REMARK 3 S11: 0.0354 S12: 0.2026 S13: 0.0865 REMARK 3 S21: -0.2173 S22: -0.1238 S23: -0.1544 REMARK 3 S31: -0.1493 S32: 0.0533 S33: 0.0887 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 12:90 REMARK 3 ORIGIN FOR THE GROUP (A): 31.9593 -4.2461 9.5515 REMARK 3 T TENSOR REMARK 3 T11: 0.1251 T22: 0.1038 REMARK 3 T33: 0.1132 T12: -0.0298 REMARK 3 T13: 0.0028 T23: 0.0149 REMARK 3 L TENSOR REMARK 3 L11: 1.7229 L22: 3.6911 REMARK 3 L33: 1.9214 L12: -0.4100 REMARK 3 L13: 0.0666 L23: 0.7761 REMARK 3 S TENSOR REMARK 3 S11: 0.0125 S12: -0.0379 S13: -0.2542 REMARK 3 S21: -0.1628 S22: -0.0033 S23: 0.0546 REMARK 3 S31: 0.1613 S32: -0.1606 S33: -0.0113 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 91:150 REMARK 3 ORIGIN FOR THE GROUP (A): 21.6530 9.7264 28.9291 REMARK 3 T TENSOR REMARK 3 T11: 0.0862 T22: 0.1641 REMARK 3 T33: 0.1007 T12: -0.0039 REMARK 3 T13: -0.0055 T23: 0.0200 REMARK 3 L TENSOR REMARK 3 L11: 3.9055 L22: 1.6648 REMARK 3 L33: 1.7353 L12: -0.3970 REMARK 3 L13: 0.1665 L23: 0.2984 REMARK 3 S TENSOR REMARK 3 S11: 0.0654 S12: -0.5113 S13: -0.1039 REMARK 3 S21: 0.0838 S22: 0.0108 S23: -0.0829 REMARK 3 S31: -0.0242 S32: 0.1089 S33: -0.0828 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND RESID 151:260 REMARK 3 ORIGIN FOR THE GROUP (A): -2.2116 7.8485 18.6020 REMARK 3 T TENSOR REMARK 3 T11: 0.0708 T22: 0.1091 REMARK 3 T33: 0.1098 T12: -0.0116 REMARK 3 T13: 0.0123 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 3.3363 L22: 2.6196 REMARK 3 L33: 1.9336 L12: 0.1105 REMARK 3 L13: 0.5511 L23: 0.0688 REMARK 3 S TENSOR REMARK 3 S11: 0.0573 S12: -0.0634 S13: -0.1644 REMARK 3 S21: -0.0700 S22: -0.0743 S23: -0.0070 REMARK 3 S31: 0.0567 S32: -0.0727 S33: 0.0237 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND RESID 261:335 REMARK 3 ORIGIN FOR THE GROUP (A): 3.6394 7.4616 -5.0053 REMARK 3 T TENSOR REMARK 3 T11: 0.3784 T22: 0.4078 REMARK 3 T33: 0.2333 T12: -0.1257 REMARK 3 T13: 0.0623 T23: -0.1257 REMARK 3 L TENSOR REMARK 3 L11: 0.7264 L22: 0.5939 REMARK 3 L33: 2.9129 L12: 0.1172 REMARK 3 L13: -0.8514 L23: -0.8583 REMARK 3 S TENSOR REMARK 3 S11: -0.2725 S12: 0.4608 S13: -0.2732 REMARK 3 S21: -0.6213 S22: 0.3190 S23: -0.2120 REMARK 3 S31: 0.2424 S32: 0.0348 S33: -0.0064 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): 18.2071 33.1314 18.4545 REMARK 3 T TENSOR REMARK 3 T11: 0.2825 T22: 0.1735 REMARK 3 T33: 0.2811 T12: -0.0567 REMARK 3 T13: -0.0481 T23: -0.0509 REMARK 3 L TENSOR REMARK 3 L11: 2.1144 L22: 6.2475 REMARK 3 L33: 4.5274 L12: 0.0505 REMARK 3 L13: -0.7394 L23: -0.8302 REMARK 3 S TENSOR REMARK 3 S11: -0.0564 S12: -0.2068 S13: 0.3762 REMARK 3 S21: -0.2927 S22: -0.3451 S23: -0.5353 REMARK 3 S31: 0.0091 S32: -0.1342 S33: 0.3262 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 9Y1D 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_1000299650. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-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) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.4.0 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91118 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 43.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.38600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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 REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 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 39.66000 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: 4000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 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 THR A 205 REMARK 465 LYS A 206 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 GLN A 8 CG CD OE1 NE2 REMARK 470 GLU A 9 CG CD OE1 OE2 REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 GLN A 207 CG CD OE1 NE2 REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 ASN A 245 CG OD1 ND2 REMARK 470 ASP A 246 CG OD1 OD2 REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 LYS A 326 CG CD CE NZ REMARK 470 GLU A 335 CG CD OE1 OE2 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 809 O HOH A 905 1.99 REMARK 500 O HOH A 798 O HOH A 878 2.01 REMARK 500 OP2 DA T 14 O HOH T 101 2.03 REMARK 500 O HOH T 117 O HOH P 103 2.04 REMARK 500 O HOH T 130 O HOH T 151 2.06 REMARK 500 O HOH T 166 O HOH T 167 2.06 REMARK 500 OE2 GLU A 71 O HOH A 501 2.10 REMARK 500 O HOH A 565 O HOH A 784 2.13 REMARK 500 NH1 ARG A 258 O HOH A 502 2.13 REMARK 500 O HOH T 135 O HOH D 123 2.17 REMARK 500 O HOH P 132 O HOH P 148 2.17 REMARK 500 OP1 DA T 6 O HOH T 102 2.18 REMARK 500 O HOH A 534 O HOH A 867 2.18 REMARK 500 O HOH A 811 O HOH A 851 2.18 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 796 O HOH A 811 1655 1.94 REMARK 500 O HOH A 880 O HOH T 108 2646 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC T 8 O3' DC T 8 C3' -0.050 REMARK 500 DG D 1 P DG D 1 OP3 -0.111 REMARK 500 DG D 4 O3' DG D 4 C3' -0.045 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 2 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA T 4 O3' - P - OP2 ANGL. DEV. = 6.8 DEGREES REMARK 500 DG T 7 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC T 16 O5' - P - OP2 ANGL. DEV. = -7.3 DEGREES REMARK 500 DC P 8 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 PRO A 50 40.83 -87.07 REMARK 500 CYS A 178 -155.72 -100.66 REMARK 500 ASN A 245 -9.20 73.55 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 91.6 REMARK 620 3 VAL A 65 O 93.5 94.8 REMARK 620 4 HOH A 814 O 86.7 91.0 174.2 REMARK 620 5 DC D 3 OP1 175.3 92.2 88.9 90.4 REMARK 620 6 HOH D 114 O 92.4 171.2 92.8 81.4 83.5 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 93.8 REMARK 620 3 ILE A 106 O 96.1 87.2 REMARK 620 4 HOH A 807 O 82.5 93.8 178.3 REMARK 620 5 DG P 9 OP1 165.5 95.4 95.5 85.7 REMARK 620 6 HOH P 119 O 80.3 173.9 91.9 86.9 90.6 REMARK 620 N 1 2 3 4 5 DBREF 9Y1D A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 9Y1D T 1 16 PDB 9Y1D 9Y1D 1 16 DBREF 9Y1D P 1 10 PDB 9Y1D 9Y1D 1 10 DBREF 9Y1D D 1 5 PDB 9Y1D 9Y1D 1 5 SEQADV 9Y1D 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 CL A 403 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 5 NA 2(NA 1+) FORMUL 7 CL CL 1- FORMUL 8 HOH *580(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 GLN A 90 1 9 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 LYS A 127 1 7 HELIX 9 AA9 ASN A 128 LEU A 132 5 5 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 SER A 229 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 2.52 LINK O VAL A 65 NA NA A 401 1555 1555 2.25 LINK O THR A 101 NA NA A 402 1555 1555 2.38 LINK O VAL A 103 NA NA A 402 1555 1555 2.51 LINK O ILE A 106 NA NA A 402 1555 1555 2.34 LINK NA NA A 401 O HOH A 814 1555 1555 2.47 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.81 LINK NA NA A 401 O HOH D 114 1555 1555 2.44 LINK NA NA A 402 O HOH A 807 1555 1555 2.50 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.35 LINK NA NA A 402 O HOH P 119 1555 1555 2.49 CISPEP 1 GLY A 274 SER A 275 0 0.15 CRYST1 54.319 79.320 54.910 90.00 105.68 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 0.018410 0.000000 0.005168 0.00000 SCALE2 0.000000 0.012607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018916 0.00000 CONECT 408 3275 CONECT 426 3275 CONECT 445 3275 CONECT 741 3276 CONECT 759 3276 CONECT 776 3276 CONECT 3108 3276 CONECT 3212 3275 CONECT 3275 408 426 445 3212 CONECT 3275 3591 3841 CONECT 3276 741 759 776 3108 CONECT 3276 3584 3795 CONECT 3584 3276 CONECT 3591 3275 CONECT 3795 3276 CONECT 3841 3275 MASTER 490 0 3 19 9 0 0 6 3804 4 16 30 END