HEADER REPLICATION 29-AUG-25 9Y1F TITLE S180R HUMAN DNA POLYMERASE BETA, BINARY COMPLEX TEMPLATING DT 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 9Y1F 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 80367 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.160 REMARK 3 FREE R VALUE TEST SET COUNT : 8167 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 39.6600 - 5.5900 0.98 2400 246 0.1581 0.1796 REMARK 3 2 5.5900 - 4.4400 0.99 2395 299 0.1486 0.1761 REMARK 3 3 4.4400 - 3.8800 0.99 2389 272 0.1329 0.1498 REMARK 3 4 3.8800 - 3.5200 0.99 2491 229 0.1429 0.1762 REMARK 3 5 3.5200 - 3.2700 0.99 2424 263 0.1549 0.1722 REMARK 3 6 3.2700 - 3.0800 0.99 2384 301 0.1609 0.1699 REMARK 3 7 3.0800 - 2.9200 0.99 2385 294 0.1791 0.2160 REMARK 3 8 2.9200 - 2.8000 0.99 2391 280 0.1819 0.2030 REMARK 3 9 2.8000 - 2.6900 0.99 2390 324 0.1735 0.2509 REMARK 3 10 2.6900 - 2.6000 0.99 2393 254 0.1841 0.1986 REMARK 3 11 2.6000 - 2.5100 1.00 2441 295 0.1792 0.2361 REMARK 3 12 2.5100 - 2.4400 0.99 2454 221 0.1701 0.2350 REMARK 3 13 2.4400 - 2.3800 1.00 2482 245 0.1809 0.2151 REMARK 3 14 2.3800 - 2.3200 1.00 2439 279 0.1690 0.1941 REMARK 3 15 2.3200 - 2.2700 0.99 2339 298 0.1693 0.2074 REMARK 3 16 2.2700 - 2.2200 0.99 2452 259 0.1666 0.2185 REMARK 3 17 2.2200 - 2.1800 0.99 2389 279 0.1697 0.2088 REMARK 3 18 2.1800 - 2.1300 0.99 2401 280 0.1679 0.2150 REMARK 3 19 2.1300 - 2.1000 0.99 2417 256 0.1816 0.2310 REMARK 3 20 2.1000 - 2.0600 0.99 2463 275 0.1912 0.2310 REMARK 3 21 2.0600 - 2.0300 0.98 2379 254 0.1888 0.2398 REMARK 3 22 2.0300 - 2.0000 0.99 2408 282 0.1936 0.2274 REMARK 3 23 2.0000 - 1.9700 0.98 2411 294 0.1886 0.2555 REMARK 3 24 1.9700 - 1.9400 0.99 2356 283 0.2058 0.2519 REMARK 3 25 1.9400 - 1.9100 0.98 2418 291 0.1995 0.2366 REMARK 3 26 1.9100 - 1.8900 0.97 2298 251 0.2058 0.2668 REMARK 3 27 1.8900 - 1.8600 0.97 2445 254 0.2296 0.2599 REMARK 3 28 1.8600 - 1.8400 0.98 2371 275 0.2445 0.2786 REMARK 3 29 1.8400 - 1.8200 0.98 2398 263 0.2549 0.2886 REMARK 3 30 1.8200 - 1.8000 0.98 2397 271 0.2552 0.3127 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.20 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 : 0.007 3363 REMARK 3 ANGLE : 0.914 4666 REMARK 3 CHIRALITY : 0.051 515 REMARK 3 PLANARITY : 0.008 495 REMARK 3 DIHEDRAL : 19.336 1321 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 1:5)) REMARK 3 ORIGIN FOR THE GROUP (A): 31.4966 9.4982 -3.2532 REMARK 3 T TENSOR REMARK 3 T11: 0.2468 T22: 0.2188 REMARK 3 T33: 0.1648 T12: 0.0097 REMARK 3 T13: 0.0312 T23: 0.0180 REMARK 3 L TENSOR REMARK 3 L11: 1.8676 L22: 2.9313 REMARK 3 L33: 2.6135 L12: -0.2995 REMARK 3 L13: -0.3526 L23: -0.3052 REMARK 3 S TENSOR REMARK 3 S11: 0.0829 S12: 0.3409 S13: 0.1636 REMARK 3 S21: -0.3375 S22: 0.0931 S23: -0.0056 REMARK 3 S31: 0.0600 S32: 0.0621 S33: -0.1154 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): 15.3500 18.1340 13.9897 REMARK 3 T TENSOR REMARK 3 T11: 0.1862 T22: 0.1495 REMARK 3 T33: 0.1914 T12: 0.0008 REMARK 3 T13: 0.0154 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 1.6821 L22: 1.5597 REMARK 3 L33: 1.9130 L12: -0.8529 REMARK 3 L13: -0.3191 L23: -0.0714 REMARK 3 S TENSOR REMARK 3 S11: 0.1579 S12: 0.0841 S13: 0.0934 REMARK 3 S21: -0.1609 S22: -0.1873 S23: -0.1004 REMARK 3 S31: -0.0913 S32: -0.0137 S33: 0.0416 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 12:90 REMARK 3 ORIGIN FOR THE GROUP (A): 31.9664 -4.3184 9.6195 REMARK 3 T TENSOR REMARK 3 T11: 0.1296 T22: 0.1186 REMARK 3 T33: 0.1470 T12: -0.0241 REMARK 3 T13: 0.0141 T23: 0.0168 REMARK 3 L TENSOR REMARK 3 L11: 1.7863 L22: 3.2513 REMARK 3 L33: 2.4805 L12: -0.1380 REMARK 3 L13: 0.2111 L23: 0.3471 REMARK 3 S TENSOR REMARK 3 S11: 0.0048 S12: -0.0743 S13: -0.2102 REMARK 3 S21: -0.1590 S22: -0.0018 S23: -0.0677 REMARK 3 S31: 0.1483 S32: -0.1134 S33: 0.0069 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 91:150 REMARK 3 ORIGIN FOR THE GROUP (A): 21.6489 9.5017 29.2822 REMARK 3 T TENSOR REMARK 3 T11: 0.1241 T22: 0.1940 REMARK 3 T33: 0.1343 T12: -0.0026 REMARK 3 T13: -0.0112 T23: 0.0190 REMARK 3 L TENSOR REMARK 3 L11: 3.7013 L22: 1.5997 REMARK 3 L33: 1.9775 L12: -0.3630 REMARK 3 L13: -0.0720 L23: 0.3543 REMARK 3 S TENSOR REMARK 3 S11: 0.0709 S12: -0.5149 S13: -0.0644 REMARK 3 S21: 0.0368 S22: 0.0114 S23: -0.1151 REMARK 3 S31: -0.0295 S32: 0.1235 S33: -0.0764 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND RESID 151:260 REMARK 3 ORIGIN FOR THE GROUP (A): -1.9630 7.8560 18.6569 REMARK 3 T TENSOR REMARK 3 T11: 0.0779 T22: 0.1391 REMARK 3 T33: 0.1446 T12: -0.0222 REMARK 3 T13: 0.0082 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 3.4085 L22: 2.9981 REMARK 3 L33: 2.2783 L12: 0.3492 REMARK 3 L13: 0.4119 L23: 0.2775 REMARK 3 S TENSOR REMARK 3 S11: 0.0557 S12: -0.0410 S13: -0.1126 REMARK 3 S21: -0.0065 S22: -0.0652 S23: 0.0533 REMARK 3 S31: 0.0265 S32: -0.1351 S33: 0.0039 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND RESID 261:335 REMARK 3 ORIGIN FOR THE GROUP (A): 3.9986 7.5365 -5.0037 REMARK 3 T TENSOR REMARK 3 T11: 0.4532 T22: 0.4375 REMARK 3 T33: 0.2561 T12: -0.2048 REMARK 3 T13: 0.0668 T23: -0.1314 REMARK 3 L TENSOR REMARK 3 L11: 0.6874 L22: 0.5789 REMARK 3 L33: 1.9277 L12: 0.2264 REMARK 3 L13: -0.8102 L23: -0.4856 REMARK 3 S TENSOR REMARK 3 S11: -0.4326 S12: 0.6089 S13: -0.3403 REMARK 3 S21: -0.7179 S22: 0.4356 S23: -0.2284 REMARK 3 S31: 0.1998 S32: -0.1432 S33: 0.0259 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): 18.4942 33.0470 18.4111 REMARK 3 T TENSOR REMARK 3 T11: 0.3517 T22: 0.1912 REMARK 3 T33: 0.3242 T12: -0.0695 REMARK 3 T13: -0.0435 T23: -0.0467 REMARK 3 L TENSOR REMARK 3 L11: 2.1305 L22: 2.9975 REMARK 3 L33: 2.7693 L12: 0.3645 REMARK 3 L13: -0.9346 L23: -0.5692 REMARK 3 S TENSOR REMARK 3 S11: 0.2106 S12: -0.1364 S13: 0.3072 REMARK 3 S21: 0.0171 S22: -0.5126 S23: -0.4552 REMARK 3 S31: -0.1584 S32: -0.2071 S33: 0.3101 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 9Y1F 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_1000299656. 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 : 7.4 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 : DIALS 3.8 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80367 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 39.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 1.15400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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 (%): 48.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 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 7.4, 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 39.66050 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: 4130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 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 465 GLN A 207 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 LYS A 113 CG CD CE NZ REMARK 470 GLU A 203 CG CD OE1 OE2 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 LYS A 331 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 OE1 GLN A 213 O HOH A 501 1.97 REMARK 500 O HOH A 632 O HOH A 739 2.03 REMARK 500 O HOH P 126 O HOH P 146 2.06 REMARK 500 O HOH T 412 O HOH P 101 2.06 REMARK 500 O HOH A 800 O HOH T 468 2.11 REMARK 500 O HOH A 767 O HOH A 799 2.13 REMARK 500 NH2 ARG A 126 O HOH A 502 2.14 REMARK 500 O HOH A 502 O HOH A 723 2.14 REMARK 500 O HOH A 605 O HOH A 788 2.15 REMARK 500 O HOH A 543 O HOH A 736 2.19 REMARK 500 O HOH T 409 O HOH T 430 2.19 REMARK 500 O HOH A 761 O HOH A 797 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 736 O HOH A 767 1655 2.07 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 -0.129 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 DG T 7 O4' - C1' - N9 ANGL. DEV. = 3.1 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 PRO A 50 44.78 -88.65 REMARK 500 CYS A 178 -158.70 -105.00 REMARK 500 ASN A 245 -11.83 73.63 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 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 90.7 REMARK 620 3 VAL A 65 O 94.4 93.7 REMARK 620 4 HOH A 742 O 88.9 82.8 175.2 REMARK 620 5 DC D 3 OP1 175.9 89.6 89.6 87.1 REMARK 620 6 HOH D 109 O 96.2 171.7 90.4 92.7 83.3 REMARK 620 N 1 2 3 4 5 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 THR A 101 O REMARK 620 2 VAL A 103 O 93.9 REMARK 620 3 ILE A 106 O 96.1 87.2 REMARK 620 4 HOH A 741 O 81.5 94.5 177.1 REMARK 620 5 DG P 9 OP1 166.3 95.4 94.4 87.7 REMARK 620 6 HOH P 115 O 82.8 175.0 89.3 88.8 88.5 REMARK 620 N 1 2 3 4 5 DBREF 9Y1F A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 9Y1F T 1 16 PDB 9Y1F 9Y1F 1 16 DBREF 9Y1F P 1 10 PDB 9Y1F 9Y1F 1 10 DBREF 9Y1F D 1 5 PDB 9Y1F 9Y1F 1 5 SEQADV 9Y1F 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 DT 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 HET CL A 404 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 5 NA 2(NA 1+) FORMUL 7 CL 2(CL 1-) FORMUL 9 HOH *494(H2 O) HELIX 1 AA1 ASN A 12 VAL A 29 1 18 HELIX 2 AA2 ALA A 32 TYR A 49 1 18 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 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 LYS A 148 1 7 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 402 1555 1555 2.30 LINK O LEU A 62 NA NA A 402 1555 1555 2.55 LINK O VAL A 65 NA NA A 402 1555 1555 2.27 LINK O THR A 101 NA NA A 401 1555 1555 2.30 LINK O VAL A 103 NA NA A 401 1555 1555 2.49 LINK O ILE A 106 NA NA A 401 1555 1555 2.37 LINK NA NA A 401 O HOH A 741 1555 1555 2.52 LINK NA NA A 401 OP1 DG P 9 1555 1555 2.38 LINK NA NA A 401 O HOH P 115 1555 1555 2.53 LINK NA NA A 402 O HOH A 742 1555 1555 2.60 LINK NA NA A 402 OP1 DC D 3 1555 1555 2.94 LINK NA NA A 402 O HOH D 109 1555 1555 2.47 CISPEP 1 GLY A 274 SER A 275 0 0.61 CRYST1 54.171 79.321 54.639 90.00 105.12 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 0.018460 0.000000 0.004988 0.00000 SCALE2 0.000000 0.012607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018958 0.00000 CONECT 419 3241 CONECT 437 3241 CONECT 456 3241 CONECT 741 3240 CONECT 759 3240 CONECT 776 3240 CONECT 3092 3240 CONECT 3177 3241 CONECT 3240 741 759 776 3092 CONECT 3240 3484 3678 CONECT 3241 419 437 456 3177 CONECT 3241 3485 3722 CONECT 3484 3240 CONECT 3485 3241 CONECT 3678 3240 CONECT 3722 3241 MASTER 483 0 4 19 9 0 0 6 3705 4 16 30 END