HEADER REPLICATION, HYDROLASE/DNA 29-AUG-25 9Y15 TITLE WT HUMAN DNA POLYMERASE BETA, BINARY COMPLEX TEMPLATING DA 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 9Y15 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. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 68373 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) : 0.168 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.260 REMARK 3 FREE R VALUE TEST SET COUNT : 7014 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 - 5.7200 0.99 2238 220 0.1401 0.1643 REMARK 3 2 5.7200 - 4.5500 1.00 2183 280 0.1392 0.1641 REMARK 3 3 4.5500 - 3.9800 1.00 2244 256 0.1252 0.1596 REMARK 3 4 3.9800 - 3.6200 1.00 2265 216 0.1378 0.1603 REMARK 3 5 3.6200 - 3.3600 1.00 2268 243 0.1457 0.1920 REMARK 3 6 3.3600 - 3.1600 1.00 2225 260 0.1533 0.1908 REMARK 3 7 3.1600 - 3.0000 0.99 2218 262 0.1766 0.2048 REMARK 3 8 3.0000 - 2.8700 0.99 2139 289 0.1865 0.2543 REMARK 3 9 2.8700 - 2.7600 0.97 2211 273 0.1791 0.2177 REMARK 3 10 2.7600 - 2.6700 0.95 2104 255 0.1739 0.2243 REMARK 3 11 2.6700 - 2.5800 0.93 2060 206 0.1735 0.2405 REMARK 3 12 2.5800 - 2.5100 0.92 2099 254 0.1741 0.2427 REMARK 3 13 2.5100 - 2.4400 0.91 2034 205 0.1756 0.2183 REMARK 3 14 2.4400 - 2.3800 0.90 2031 199 0.1764 0.2388 REMARK 3 15 2.3800 - 2.3300 0.90 2032 232 0.1762 0.2211 REMARK 3 16 2.3300 - 2.2800 0.89 1932 240 0.1737 0.2142 REMARK 3 17 2.2800 - 2.2400 0.89 2016 236 0.1730 0.2435 REMARK 3 18 2.2400 - 2.1900 0.88 1964 223 0.1764 0.2392 REMARK 3 19 2.1900 - 2.1500 0.88 1990 223 0.1818 0.2208 REMARK 3 20 2.1500 - 2.1200 0.88 1946 230 0.1891 0.2483 REMARK 3 21 2.1200 - 2.0800 0.87 1912 220 0.1939 0.2608 REMARK 3 22 2.0800 - 2.0500 0.87 1996 227 0.1909 0.2443 REMARK 3 23 2.0500 - 2.0200 0.85 1897 176 0.1970 0.2613 REMARK 3 24 2.0200 - 1.9900 0.86 1922 246 0.2050 0.2462 REMARK 3 25 1.9900 - 1.9700 0.85 1880 229 0.2012 0.2477 REMARK 3 26 1.9700 - 1.9400 0.86 1904 220 0.2259 0.3015 REMARK 3 27 1.9400 - 1.9200 0.86 1901 229 0.2294 0.2498 REMARK 3 28 1.9200 - 1.8900 0.85 1932 234 0.2316 0.3041 REMARK 3 29 1.8900 - 1.8700 0.85 1874 208 0.2520 0.2958 REMARK 3 30 1.8700 - 1.8500 0.84 1942 223 0.2508 0.2871 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.30 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 3376 REMARK 3 ANGLE : 0.906 4686 REMARK 3 CHIRALITY : 0.052 518 REMARK 3 PLANARITY : 0.009 493 REMARK 3 DIHEDRAL : 19.919 1337 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): 32.0668 -4.0940 9.7472 REMARK 3 T TENSOR REMARK 3 T11: 0.1451 T22: 0.0846 REMARK 3 T33: 0.1167 T12: -0.0235 REMARK 3 T13: 0.0044 T23: 0.0256 REMARK 3 L TENSOR REMARK 3 L11: 0.7761 L22: 1.8515 REMARK 3 L33: 0.8951 L12: -0.1162 REMARK 3 L13: -0.0516 L23: 0.5544 REMARK 3 S TENSOR REMARK 3 S11: 0.0043 S12: -0.0833 S13: -0.1624 REMARK 3 S21: -0.1187 S22: 0.0469 S23: -0.0967 REMARK 3 S31: 0.1627 S32: -0.0667 S33: -0.0387 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 91:150 REMARK 3 ORIGIN FOR THE GROUP (A): 22.0616 9.3841 29.1335 REMARK 3 T TENSOR REMARK 3 T11: 0.0849 T22: 0.1660 REMARK 3 T33: 0.1007 T12: -0.0013 REMARK 3 T13: -0.0046 T23: 0.0162 REMARK 3 L TENSOR REMARK 3 L11: 2.2305 L22: 0.8993 REMARK 3 L33: 1.3185 L12: 0.0014 REMARK 3 L13: -0.2317 L23: -0.1306 REMARK 3 S TENSOR REMARK 3 S11: 0.0362 S12: -0.5223 S13: -0.0843 REMARK 3 S21: 0.0784 S22: 0.0324 S23: 0.0258 REMARK 3 S31: 0.0170 S32: 0.1034 S33: -0.0572 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 151:260 REMARK 3 ORIGIN FOR THE GROUP (A): -1.6238 8.1400 18.4048 REMARK 3 T TENSOR REMARK 3 T11: 0.0787 T22: 0.1116 REMARK 3 T33: 0.1391 T12: -0.0163 REMARK 3 T13: 0.0113 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 1.7176 L22: 0.8745 REMARK 3 L33: 1.5660 L12: 0.0362 REMARK 3 L13: 0.1060 L23: 0.1282 REMARK 3 S TENSOR REMARK 3 S11: 0.1389 S12: -0.0078 S13: -0.1037 REMARK 3 S21: -0.0162 S22: -0.0287 S23: -0.0212 REMARK 3 S31: -0.0448 S32: -0.0825 S33: -0.0938 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 261:335 REMARK 3 ORIGIN FOR THE GROUP (A): 3.8855 6.9927 -4.8392 REMARK 3 T TENSOR REMARK 3 T11: 0.3481 T22: 0.6408 REMARK 3 T33: 0.1745 T12: -0.2025 REMARK 3 T13: 0.0586 T23: -0.2613 REMARK 3 L TENSOR REMARK 3 L11: 0.1713 L22: 0.2485 REMARK 3 L33: 0.5692 L12: -0.0028 REMARK 3 L13: 0.0109 L23: -0.1394 REMARK 3 S TENSOR REMARK 3 S11: -0.1715 S12: 0.4586 S13: -0.2093 REMARK 3 S21: -0.4674 S22: 0.2559 S23: -0.1528 REMARK 3 S31: 0.1241 S32: 0.0007 S33: 0.0470 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): 31.8648 9.4635 -3.2671 REMARK 3 T TENSOR REMARK 3 T11: 0.1661 T22: 0.1285 REMARK 3 T33: 0.1124 T12: -0.0100 REMARK 3 T13: 0.0204 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 1.3431 L22: 2.7365 REMARK 3 L33: 3.5274 L12: -1.1985 REMARK 3 L13: -0.1607 L23: -0.4879 REMARK 3 S TENSOR REMARK 3 S11: 0.0816 S12: 0.2275 S13: 0.1802 REMARK 3 S21: -0.1583 S22: -0.0045 S23: -0.1359 REMARK 3 S31: -0.0772 S32: 0.1016 S33: -0.0422 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): 15.2884 16.8515 14.0829 REMARK 3 T TENSOR REMARK 3 T11: 0.1499 T22: 0.0969 REMARK 3 T33: 0.1254 T12: 0.0024 REMARK 3 T13: 0.0116 T23: 0.0155 REMARK 3 L TENSOR REMARK 3 L11: 1.4376 L22: 1.5981 REMARK 3 L33: 1.6704 L12: -0.6427 REMARK 3 L13: 0.5162 L23: 0.0921 REMARK 3 S TENSOR REMARK 3 S11: 0.1337 S12: 0.2396 S13: 0.1078 REMARK 3 S21: -0.1326 S22: -0.1413 S23: -0.0627 REMARK 3 S31: -0.1134 S32: 0.0485 S33: 0.0147 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): 18.9311 32.6176 18.3040 REMARK 3 T TENSOR REMARK 3 T11: 0.2807 T22: 0.1628 REMARK 3 T33: 0.2539 T12: -0.0725 REMARK 3 T13: -0.0468 T23: -0.0398 REMARK 3 L TENSOR REMARK 3 L11: 1.3564 L22: 3.2238 REMARK 3 L33: 2.5596 L12: 0.6180 REMARK 3 L13: -0.6484 L23: 0.5219 REMARK 3 S TENSOR REMARK 3 S11: -0.0064 S12: -0.0788 S13: 0.1746 REMARK 3 S21: -0.0415 S22: -0.1914 S23: -0.2760 REMARK 3 S31: -0.1053 S32: -0.0446 S33: 0.1276 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 9Y15 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_1000299599. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER IMUS MICROFOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS 3 REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS 3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68373 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.55 REMARK 200 R MERGE FOR SHELL (I) : 0.39700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 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 (%): 48.16 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 7.5, 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 39.29750 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: 4210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 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 LYS A 244 REMARK 465 ASN A 245 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 GLN A 207 CG CD OE1 NE2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 ASP A 246 CG OD1 OD2 REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 LYS A 248 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 A 782 O HOH A 883 1.99 REMARK 500 O HOH P 115 O HOH P 142 2.06 REMARK 500 O HOH T 105 O HOH D 135 2.10 REMARK 500 O HOH A 762 O HOH A 883 2.14 REMARK 500 NH1 ARG A 40 O HOH A 501 2.15 REMARK 500 O HOH A 909 O HOH T 158 2.17 REMARK 500 O HOH T 101 O HOH T 162 2.17 REMARK 500 O HOH A 656 O HOH A 708 2.17 REMARK 500 O HOH A 592 O HOH A 885 2.18 REMARK 500 O HOH A 506 O HOH A 836 2.18 REMARK 500 OE1 GLU A 153 O HOH A 502 2.18 REMARK 500 O HOH A 603 O HOH A 773 2.19 REMARK 500 O HOH A 560 O HOH A 886 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 708 O HOH A 891 1655 2.08 REMARK 500 O HOH A 767 O HOH A 838 2655 2.16 REMARK 500 O HOH A 637 O HOH P 136 2646 2.18 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 -0.130 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. = 2.6 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 44.00 -85.95 REMARK 500 CYS A 178 -156.27 -98.51 REMARK 500 ASN A 294 -168.46 -126.94 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 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 30 O REMARK 620 2 SER A 171 OG 39.9 REMARK 620 3 HOH A 578 O 43.2 3.8 REMARK 620 4 HOH A 769 O 40.2 3.5 3.5 REMARK 620 5 HOH A 787 O 42.1 2.1 2.1 3.9 REMARK 620 6 HOH A 818 O 42.1 4.3 2.1 1.9 3.6 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 LYS A 60 O REMARK 620 2 LEU A 62 O 91.4 REMARK 620 3 VAL A 65 O 91.4 97.2 REMARK 620 4 HOH A 820 O 90.3 85.2 177.0 REMARK 620 5 DC D 3 OP1 177.3 91.2 88.2 90.0 REMARK 620 6 HOH D 113 O 93.3 171.5 89.7 87.7 84.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 VAL A 103 O 95.2 REMARK 620 3 ILE A 106 O 92.7 86.9 REMARK 620 4 HOH A 811 O 86.1 93.6 178.7 REMARK 620 5 DG P 9 OP1 168.2 94.9 93.9 87.2 REMARK 620 6 HOH P 129 O 77.2 171.2 89.1 90.3 93.2 REMARK 620 N 1 2 3 4 5 DBREF 9Y15 A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 9Y15 T 1 16 PDB 9Y15 9Y15 1 16 DBREF 9Y15 P 1 10 PDB 9Y15 9Y15 1 10 DBREF 9Y15 D 1 5 PDB 9Y15 9Y15 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 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 NA A 403 1 HET CL A 404 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 5 NA 3(NA 1+) FORMUL 8 CL CL 1- FORMUL 9 HOH *582(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 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 THR A 225 O VAL A 238 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 SER A 30 NA NA A 403 1555 1655 2.33 LINK O LYS A 60 NA NA A 401 1555 1555 2.29 LINK O LEU A 62 NA NA A 401 1555 1555 2.48 LINK O VAL A 65 NA NA A 401 1555 1555 2.36 LINK O THR A 101 NA NA A 402 1555 1555 2.31 LINK O VAL A 103 NA NA A 402 1555 1555 2.41 LINK O ILE A 106 NA NA A 402 1555 1555 2.37 LINK OG SER A 171 NA NA A 403 1555 1555 2.34 LINK NA NA A 401 O HOH A 820 1555 1555 2.44 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.71 LINK NA NA A 401 O HOH D 113 1555 1555 2.33 LINK NA NA A 402 O HOH A 811 1555 1555 2.45 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.34 LINK NA NA A 402 O HOH P 129 1555 1555 2.46 LINK NA NA A 403 O HOH A 578 1555 1555 2.58 LINK NA NA A 403 O HOH A 769 1555 1555 2.28 LINK NA NA A 403 O HOH A 787 1555 1455 2.32 LINK NA NA A 403 O HOH A 818 1555 1455 2.43 CISPEP 1 GLY A 274 SER A 275 0 1.91 CRYST1 54.333 78.595 54.771 90.00 104.62 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 0.018405 0.000000 0.004801 0.00000 SCALE2 0.000000 0.012723 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018869 0.00000 CONECT 402 3251 CONECT 420 3251 CONECT 439 3251 CONECT 730 3252 CONECT 748 3252 CONECT 765 3252 CONECT 1309 3253 CONECT 3084 3252 CONECT 3188 3251 CONECT 3251 402 420 439 3188 CONECT 3251 3574 3810 CONECT 3252 730 748 765 3084 CONECT 3252 3565 3780 CONECT 3253 1309 3332 3523 CONECT 3332 3253 CONECT 3523 3253 CONECT 3565 3252 CONECT 3574 3251 CONECT 3780 3252 CONECT 3810 3251 MASTER 495 0 4 19 9 0 0 6 3784 4 20 30 END