HEADER REPLICATION, HYDROLASE/DNA 29-AUG-25 9Y18 TITLE WT HUMAN DNA POLYMERASE BETA, BINARY COMPLEX TEMPLATING DC COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7,4.2.99.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TEMPLATE STRAND; COMPND 8 CHAIN: T; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: PRIMER STRAND; COMPND 12 CHAIN: P; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: DOWNSTREAM; COMPND 16 CHAIN: D; COMPND 17 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, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.E.ECKENROTH,S.DOUBLIE REVDAT 1 28-JAN-26 9Y18 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) : 23.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 80642 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.150 REMARK 3 FREE R VALUE TEST SET COUNT : 8189 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 23.4500 - 5.5700 0.99 2420 248 0.1437 0.1704 REMARK 3 2 5.5700 - 4.4300 1.00 2430 287 0.1364 0.1628 REMARK 3 3 4.4300 - 3.8700 1.00 2376 285 0.1282 0.1497 REMARK 3 4 3.8700 - 3.5200 1.00 2472 225 0.1400 0.1462 REMARK 3 5 3.5200 - 3.2700 1.00 2463 260 0.1465 0.1840 REMARK 3 6 3.2700 - 3.0800 1.00 2388 292 0.1591 0.2030 REMARK 3 7 3.0800 - 2.9200 1.00 2410 316 0.1766 0.2153 REMARK 3 8 2.9200 - 2.8000 1.00 2374 284 0.1694 0.2184 REMARK 3 9 2.8000 - 2.6900 1.00 2423 291 0.1748 0.2309 REMARK 3 10 2.6900 - 2.6000 1.00 2396 282 0.1679 0.2275 REMARK 3 11 2.6000 - 2.5100 1.00 2416 283 0.1666 0.2215 REMARK 3 12 2.5100 - 2.4400 1.00 2443 240 0.1765 0.2224 REMARK 3 13 2.4400 - 2.3800 1.00 2439 227 0.1679 0.2352 REMARK 3 14 2.3800 - 2.3200 1.00 2457 295 0.1650 0.1950 REMARK 3 15 2.3200 - 2.2700 1.00 2363 277 0.1698 0.2206 REMARK 3 16 2.2700 - 2.2200 1.00 2436 270 0.1624 0.2268 REMARK 3 17 2.2200 - 2.1800 1.00 2423 263 0.1638 0.2026 REMARK 3 18 2.1700 - 2.1300 1.00 2451 287 0.1675 0.1983 REMARK 3 19 2.1300 - 2.1000 1.00 2351 290 0.1683 0.2284 REMARK 3 20 2.1000 - 2.0600 1.00 2465 251 0.1745 0.2254 REMARK 3 21 2.0600 - 2.0300 1.00 2403 252 0.1767 0.2549 REMARK 3 22 2.0300 - 2.0000 1.00 2436 287 0.1870 0.2286 REMARK 3 23 2.0000 - 1.9700 1.00 2396 300 0.1840 0.2541 REMARK 3 24 1.9700 - 1.9400 1.00 2404 272 0.1935 0.2594 REMARK 3 25 1.9400 - 1.9100 1.00 2383 278 0.1884 0.2195 REMARK 3 26 1.9100 - 1.8900 0.99 2440 284 0.1938 0.2634 REMARK 3 27 1.8900 - 1.8600 1.00 2425 262 0.2050 0.2531 REMARK 3 28 1.8600 - 1.8400 1.00 2400 274 0.2003 0.2563 REMARK 3 29 1.8400 - 1.8200 1.00 2414 266 0.2120 0.2514 REMARK 3 30 1.8200 - 1.8000 0.98 2356 261 0.2110 0.2595 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 3330 REMARK 3 ANGLE : 0.844 4624 REMARK 3 CHIRALITY : 0.052 512 REMARK 3 PLANARITY : 0.008 488 REMARK 3 DIHEDRAL : 19.464 1310 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID 12:90 REMARK 3 ORIGIN FOR THE GROUP (A): 32.3002 -4.3208 9.6556 REMARK 3 T TENSOR REMARK 3 T11: 0.1236 T22: 0.0627 REMARK 3 T33: 0.1111 T12: -0.0153 REMARK 3 T13: 0.0046 T23: 0.0208 REMARK 3 L TENSOR REMARK 3 L11: 0.8018 L22: 1.6241 REMARK 3 L33: 0.8214 L12: -0.1590 REMARK 3 L13: -0.0017 L23: 0.5061 REMARK 3 S TENSOR REMARK 3 S11: 0.0311 S12: -0.0794 S13: -0.1930 REMARK 3 S21: -0.0775 S22: 0.0162 S23: -0.1121 REMARK 3 S31: 0.1898 S32: -0.0362 S33: -0.0488 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 91:150 REMARK 3 ORIGIN FOR THE GROUP (A): 22.3149 9.5048 29.1019 REMARK 3 T TENSOR REMARK 3 T11: 0.0694 T22: 0.1503 REMARK 3 T33: 0.0777 T12: -0.0004 REMARK 3 T13: -0.0080 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 2.0666 L22: 0.4553 REMARK 3 L33: 0.8983 L12: 0.0144 REMARK 3 L13: -0.3249 L23: 0.0341 REMARK 3 S TENSOR REMARK 3 S11: 0.0335 S12: -0.5932 S13: -0.1051 REMARK 3 S21: 0.0960 S22: 0.0135 S23: -0.0036 REMARK 3 S31: 0.0314 S32: 0.1382 S33: -0.0439 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 151:260 REMARK 3 ORIGIN FOR THE GROUP (A): -1.5999 8.0157 18.2707 REMARK 3 T TENSOR REMARK 3 T11: 0.0398 T22: 0.0788 REMARK 3 T33: 0.0937 T12: -0.0096 REMARK 3 T13: 0.0099 T23: 0.0056 REMARK 3 L TENSOR REMARK 3 L11: 2.7377 L22: 1.5667 REMARK 3 L33: 1.7552 L12: 0.4033 REMARK 3 L13: 0.0547 L23: 0.3774 REMARK 3 S TENSOR REMARK 3 S11: 0.0788 S12: -0.0510 S13: -0.0769 REMARK 3 S21: -0.0016 S22: -0.0320 S23: -0.0559 REMARK 3 S31: 0.0249 S32: -0.0675 S33: -0.0237 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 261:335 REMARK 3 ORIGIN FOR THE GROUP (A): 4.0175 7.2404 -4.8612 REMARK 3 T TENSOR REMARK 3 T11: 0.3755 T22: 0.5408 REMARK 3 T33: 0.0954 T12: -0.2533 REMARK 3 T13: 0.0949 T23: -0.3029 REMARK 3 L TENSOR REMARK 3 L11: 0.8443 L22: 0.7334 REMARK 3 L33: 0.9857 L12: 0.2648 REMARK 3 L13: -0.2989 L23: -0.2099 REMARK 3 S TENSOR REMARK 3 S11: -0.4537 S12: 0.7774 S13: -0.6027 REMARK 3 S21: -0.7362 S22: 0.5126 S23: -0.2789 REMARK 3 S31: 0.4136 S32: -0.1570 S33: 0.0979 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ((CHAIN T AND RESID 1:5) OR (CHAIN D AND RESID 1:5)) REMARK 3 ORIGIN FOR THE GROUP (A): 31.7379 9.4129 -3.2497 REMARK 3 T TENSOR REMARK 3 T11: 0.1407 T22: 0.1006 REMARK 3 T33: 0.0996 T12: -0.0061 REMARK 3 T13: 0.0318 T23: 0.0244 REMARK 3 L TENSOR REMARK 3 L11: 1.7654 L22: 2.3780 REMARK 3 L33: 3.9226 L12: -0.9107 REMARK 3 L13: 0.8189 L23: -0.3711 REMARK 3 S TENSOR REMARK 3 S11: 0.0931 S12: 0.2573 S13: 0.1906 REMARK 3 S21: -0.2986 S22: 0.0207 S23: -0.1524 REMARK 3 S31: -0.1001 S32: 0.1001 S33: -0.0931 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ((CHAIN T AND RESID 7:11) OR (CHAIN P AND RESID REMARK 3 6:10)) REMARK 3 ORIGIN FOR THE GROUP (A): 15.3129 16.8160 14.0838 REMARK 3 T TENSOR REMARK 3 T11: 0.0981 T22: 0.0726 REMARK 3 T33: 0.1058 T12: 0.0107 REMARK 3 T13: 0.0089 T23: 0.0286 REMARK 3 L TENSOR REMARK 3 L11: 2.1950 L22: 1.2957 REMARK 3 L33: 2.0299 L12: -0.4066 REMARK 3 L13: 0.3875 L23: 0.4549 REMARK 3 S TENSOR REMARK 3 S11: 0.1499 S12: 0.2712 S13: 0.2187 REMARK 3 S21: -0.0936 S22: -0.1891 S23: -0.0605 REMARK 3 S31: -0.1618 S32: 0.0387 S33: 0.0001 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ((CHAIN T AND RESID 12:16) OR (CHAIN P AND RESID REMARK 3 1:5)) REMARK 3 ORIGIN FOR THE GROUP (A): 18.9758 32.5739 18.2785 REMARK 3 T TENSOR REMARK 3 T11: 0.3142 T22: 0.1447 REMARK 3 T33: 0.2764 T12: -0.0549 REMARK 3 T13: -0.0247 T23: -0.0556 REMARK 3 L TENSOR REMARK 3 L11: 1.9500 L22: 3.4043 REMARK 3 L33: 2.4634 L12: 0.2594 REMARK 3 L13: -0.1093 L23: 0.0807 REMARK 3 S TENSOR REMARK 3 S11: 0.0680 S12: -0.1720 S13: 0.3105 REMARK 3 S21: -0.0724 S22: -0.2841 S23: -0.5076 REMARK 3 S31: -0.0481 S32: -0.2060 S33: 0.1527 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 9Y18 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_1000299614. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-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 : SAINT 3 REMARK 200 DATA SCALING SOFTWARE : SAINT 3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80642 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.870 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.6000 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) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.25800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.000 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 (%): 47.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 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 39.22950 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: 4280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 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 THR A 205 REMARK 465 LYS A 206 REMARK 465 GLN A 207 REMARK 465 PRO A 208 REMARK 465 ASN A 245 REMARK 465 ASP A 246 REMARK 465 GLU A 247 REMARK 465 LYS A 248 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 GLU A 9 CG CD OE1 OE2 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 LYS A 326 CG CD CE NZ 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 P 125 O HOH P 143 2.00 REMARK 500 O HOH A 799 O HOH A 897 2.01 REMARK 500 O HOH T 116 O HOH T 150 2.02 REMARK 500 O HOH T 125 O HOH D 134 2.07 REMARK 500 O HOH D 116 O HOH D 139 2.12 REMARK 500 O HOH A 872 O HOH A 875 2.12 REMARK 500 O HOH A 674 O HOH A 905 2.12 REMARK 500 O HOH A 761 O HOH A 834 2.14 REMARK 500 O HOH A 908 O HOH T 175 2.14 REMARK 500 O HOH A 602 O HOH D 110 2.14 REMARK 500 O HOH A 659 O HOH A 787 2.14 REMARK 500 NH2 ARG A 126 O HOH A 501 2.16 REMARK 500 OP1 DG D 5 O HOH D 101 2.16 REMARK 500 O HOH A 828 O HOH A 871 2.16 REMARK 500 O HOH P 125 O HOH P 151 2.18 REMARK 500 O HOH P 143 O HOH P 151 2.19 REMARK 500 O HOH T 103 O HOH T 182 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 784 O HOH A 884 1655 2.12 REMARK 500 O HOH A 746 O HOH A 910 1455 2.16 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 -0.125 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. = 1.9 DEGREES REMARK 500 DG T 7 O4' - C1' - N9 ANGL. DEV. = 2.5 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 43.19 -87.34 REMARK 500 CYS A 178 -153.73 -103.69 REMARK 500 ASN A 294 -167.66 -128.64 REMARK 500 ARG A 333 31.40 -93.91 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 93.7 REMARK 620 3 VAL A 65 O 92.8 94.5 REMARK 620 4 HOH A 815 O 92.3 83.9 174.7 REMARK 620 5 DC D 3 OP1 176.8 89.1 88.6 86.3 REMARK 620 6 HOH D 114 O 93.7 171.3 89.7 91.2 83.4 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 93.4 REMARK 620 3 ILE A 106 O 91.9 87.2 REMARK 620 4 HOH A 812 O 84.8 95.5 175.8 REMARK 620 5 DG P 9 OP1 168.0 96.9 94.7 88.2 REMARK 620 6 HOH P 124 O 78.8 171.5 89.6 87.3 91.2 REMARK 620 N 1 2 3 4 5 DBREF 9Y18 A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 9Y18 T 1 16 PDB 9Y18 9Y18 1 16 DBREF 9Y18 P 1 10 PDB 9Y18 9Y18 1 10 DBREF 9Y18 D 1 5 PDB 9Y18 9Y18 1 5 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 SER 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 DC 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 *635(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 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 LEU A 210 VAL A 221 1 12 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 2.27 LINK O LEU A 62 NA NA A 401 1555 1555 2.54 LINK O VAL A 65 NA NA A 401 1555 1555 2.29 LINK O THR A 101 NA NA A 402 1555 1555 2.32 LINK O VAL A 103 NA NA A 402 1555 1555 2.42 LINK O ILE A 106 NA NA A 402 1555 1555 2.42 LINK NA NA A 401 O HOH A 815 1555 1555 2.49 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.76 LINK NA NA A 401 O HOH D 114 1555 1555 2.35 LINK NA NA A 402 O HOH A 812 1555 1555 2.47 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.36 LINK NA NA A 402 O HOH P 124 1555 1555 2.51 CISPEP 1 GLY A 274 SER A 275 0 3.82 CRYST1 54.136 78.459 54.727 90.00 104.36 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 0.018472 0.000000 0.004729 0.00000 SCALE2 0.000000 0.012746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018862 0.00000 CONECT 395 3209 CONECT 413 3209 CONECT 432 3209 CONECT 723 3210 CONECT 741 3210 CONECT 758 3210 CONECT 3042 3210 CONECT 3146 3209 CONECT 3209 395 413 432 3146 CONECT 3209 3527 3821 CONECT 3210 723 741 758 3042 CONECT 3210 3524 3780 CONECT 3524 3210 CONECT 3527 3209 CONECT 3780 3210 CONECT 3821 3209 MASTER 493 0 4 19 9 0 0 6 3801 4 16 30 END