HEADER REPLICATION, HYDROLASE/DNA 29-AUG-25 9Y16 TITLE WT HUMAN DNA POLYMERASE BETA, BINARY COMPLEX TEMPLATING DG 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 9Y16 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 (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 80425 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.160 REMARK 3 FREE R VALUE TEST SET COUNT : 8169 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 2410 246 0.1424 0.1577 REMARK 3 2 5.5700 - 4.4300 1.00 2398 291 0.1385 0.1624 REMARK 3 3 4.4300 - 3.8700 1.00 2395 287 0.1251 0.1465 REMARK 3 4 3.8700 - 3.5200 1.00 2461 219 0.1431 0.1739 REMARK 3 5 3.5200 - 3.2700 1.00 2441 260 0.1511 0.1729 REMARK 3 6 3.2700 - 3.0800 1.00 2393 299 0.1646 0.1839 REMARK 3 7 3.0800 - 2.9200 1.00 2395 301 0.1784 0.2407 REMARK 3 8 2.9200 - 2.8000 1.00 2377 286 0.1810 0.2129 REMARK 3 9 2.8000 - 2.6900 1.00 2412 297 0.1797 0.2348 REMARK 3 10 2.6900 - 2.6000 1.00 2389 276 0.1769 0.2563 REMARK 3 11 2.6000 - 2.5100 1.00 2381 291 0.1758 0.2495 REMARK 3 12 2.5100 - 2.4400 1.00 2430 227 0.1845 0.2370 REMARK 3 13 2.4400 - 2.3800 1.00 2433 235 0.1834 0.2269 REMARK 3 14 2.3800 - 2.3200 1.00 2488 276 0.1744 0.2227 REMARK 3 15 2.3200 - 2.2700 1.00 2352 291 0.1779 0.2214 REMARK 3 16 2.2700 - 2.2200 1.00 2438 272 0.1763 0.2472 REMARK 3 17 2.2200 - 2.1700 1.00 2405 272 0.1822 0.2167 REMARK 3 18 2.1700 - 2.1300 1.00 2444 267 0.1742 0.2083 REMARK 3 19 2.1300 - 2.1000 1.00 2357 285 0.1941 0.2457 REMARK 3 20 2.1000 - 2.0600 1.00 2445 264 0.1856 0.2483 REMARK 3 21 2.0600 - 2.0300 1.00 2412 262 0.1907 0.2248 REMARK 3 22 2.0300 - 2.0000 1.00 2402 271 0.1987 0.2515 REMARK 3 23 2.0000 - 1.9700 1.00 2414 295 0.1927 0.2403 REMARK 3 24 1.9700 - 1.9400 1.00 2403 278 0.2046 0.2482 REMARK 3 25 1.9400 - 1.9100 1.00 2376 280 0.2040 0.2361 REMARK 3 26 1.9100 - 1.8900 1.00 2423 280 0.2165 0.2786 REMARK 3 27 1.8900 - 1.8600 1.00 2391 275 0.2292 0.2675 REMARK 3 28 1.8600 - 1.8400 1.00 2413 268 0.2334 0.2623 REMARK 3 29 1.8400 - 1.8200 1.00 2441 273 0.2526 0.2979 REMARK 3 30 1.8200 - 1.8000 0.97 2337 245 0.2645 0.3397 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) : 21.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 3358 REMARK 3 ANGLE : 0.864 4660 REMARK 3 CHIRALITY : 0.053 514 REMARK 3 PLANARITY : 0.009 490 REMARK 3 DIHEDRAL : 19.906 1320 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): 31.7526 -4.0646 9.6684 REMARK 3 T TENSOR REMARK 3 T11: 0.1204 T22: 0.0874 REMARK 3 T33: 0.1295 T12: -0.0193 REMARK 3 T13: 0.0014 T23: 0.0312 REMARK 3 L TENSOR REMARK 3 L11: 1.5544 L22: 4.0068 REMARK 3 L33: 2.1849 L12: -0.0329 REMARK 3 L13: 0.0389 L23: 1.3059 REMARK 3 S TENSOR REMARK 3 S11: 0.0445 S12: -0.1372 S13: -0.2422 REMARK 3 S21: -0.0791 S22: -0.0102 S23: -0.1626 REMARK 3 S31: 0.2011 S32: -0.0429 S33: -0.0318 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 91:150 REMARK 3 ORIGIN FOR THE GROUP (A): 22.0148 9.6694 29.1255 REMARK 3 T TENSOR REMARK 3 T11: 0.0889 T22: 0.1942 REMARK 3 T33: 0.1210 T12: -0.0085 REMARK 3 T13: -0.0145 T23: 0.0128 REMARK 3 L TENSOR REMARK 3 L11: 3.3307 L22: 1.0776 REMARK 3 L33: 1.7317 L12: -0.2023 REMARK 3 L13: -0.1118 L23: 0.0754 REMARK 3 S TENSOR REMARK 3 S11: 0.0104 S12: -0.6968 S13: -0.1286 REMARK 3 S21: 0.1396 S22: 0.0355 S23: -0.0638 REMARK 3 S31: -0.0389 S32: 0.1936 S33: -0.0516 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 151:260 REMARK 3 ORIGIN FOR THE GROUP (A): -1.6561 7.9644 18.5165 REMARK 3 T TENSOR REMARK 3 T11: 0.0608 T22: 0.1042 REMARK 3 T33: 0.1285 T12: -0.0175 REMARK 3 T13: 0.0143 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 4.2320 L22: 2.2440 REMARK 3 L33: 2.3190 L12: 0.0832 REMARK 3 L13: 0.0712 L23: 0.2240 REMARK 3 S TENSOR REMARK 3 S11: 0.1357 S12: -0.0780 S13: -0.0772 REMARK 3 S21: -0.0692 S22: -0.0253 S23: -0.0661 REMARK 3 S31: -0.0348 S32: -0.0417 S33: -0.0809 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 261:335 REMARK 3 ORIGIN FOR THE GROUP (A): 3.9776 7.0641 -4.7601 REMARK 3 T TENSOR REMARK 3 T11: 0.4590 T22: 0.7435 REMARK 3 T33: 0.1964 T12: -0.2407 REMARK 3 T13: 0.0962 T23: -0.3591 REMARK 3 L TENSOR REMARK 3 L11: 1.4394 L22: 0.6086 REMARK 3 L33: 2.1693 L12: -0.0031 REMARK 3 L13: -0.5154 L23: -0.3478 REMARK 3 S TENSOR REMARK 3 S11: -0.4055 S12: 1.0109 S13: -0.7439 REMARK 3 S21: -0.7788 S22: 0.6843 S23: -0.2896 REMARK 3 S31: 0.2907 S32: -0.1135 S33: 0.1699 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): 31.8551 9.6352 -3.1908 REMARK 3 T TENSOR REMARK 3 T11: 0.1459 T22: 0.1130 REMARK 3 T33: 0.1083 T12: 0.0104 REMARK 3 T13: 0.0092 T23: 0.0186 REMARK 3 L TENSOR REMARK 3 L11: 4.0657 L22: 5.3129 REMARK 3 L33: 7.7506 L12: -1.8226 REMARK 3 L13: 0.2141 L23: -1.1409 REMARK 3 S TENSOR REMARK 3 S11: 0.1297 S12: 0.3453 S13: 0.2968 REMARK 3 S21: -0.2493 S22: -0.0002 S23: -0.1148 REMARK 3 S31: -0.0276 S32: 0.0749 S33: -0.1134 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): 15.2209 16.8293 14.0479 REMARK 3 T TENSOR REMARK 3 T11: 0.1307 T22: 0.1065 REMARK 3 T33: 0.1319 T12: 0.0134 REMARK 3 T13: 0.0131 T23: 0.0124 REMARK 3 L TENSOR REMARK 3 L11: 6.3608 L22: 4.3135 REMARK 3 L33: 4.2947 L12: 0.9036 REMARK 3 L13: -0.1599 L23: -0.2594 REMARK 3 S TENSOR REMARK 3 S11: 0.1984 S12: 0.5255 S13: 0.2240 REMARK 3 S21: -0.2912 S22: -0.1784 S23: 0.0163 REMARK 3 S31: -0.1387 S32: -0.0472 S33: -0.0345 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): 18.7095 32.7273 18.2201 REMARK 3 T TENSOR REMARK 3 T11: 0.2870 T22: 0.1435 REMARK 3 T33: 0.2969 T12: -0.0632 REMARK 3 T13: -0.0386 T23: -0.0359 REMARK 3 L TENSOR REMARK 3 L11: 2.9560 L22: 9.3927 REMARK 3 L33: 5.7111 L12: 1.1983 REMARK 3 L13: 0.2069 L23: 0.7931 REMARK 3 S TENSOR REMARK 3 S11: -0.0714 S12: -0.1150 S13: 0.3432 REMARK 3 S21: -0.1705 S22: -0.3768 S23: -0.4909 REMARK 3 S31: 0.1365 S32: -0.1939 S33: 0.3999 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 9Y16 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_1000299608. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-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 : 80425 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.05600 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.25 REMARK 200 R MERGE FOR SHELL (I) : 0.42200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 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 (%): 47.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 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 39.24400 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: 4330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 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 SER A 204 REMARK 465 THR A 205 REMARK 465 LYS A 206 REMARK 465 GLN A 207 REMARK 465 LYS A 244 REMARK 465 ASN A 245 REMARK 465 ASP A 246 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 209 CG CD CE NZ REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 GLN A 324 CG CD OE1 NE2 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 778 O HOH A 856 2.08 REMARK 500 O HOH A 749 O HOH A 771 2.11 REMARK 500 O HOH A 528 O HOH T 152 2.11 REMARK 500 O HOH A 792 O HOH A 799 2.12 REMARK 500 O HOH A 597 O HOH A 850 2.14 REMARK 500 O HOH A 607 O HOH A 665 2.16 REMARK 500 O HOH A 504 O HOH A 574 2.17 REMARK 500 OP2 DG T 9 O HOH T 101 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 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 DC T 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG T 7 O4' - C1' - N9 ANGL. DEV. = 2.2 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 44.30 -85.54 REMARK 500 GLU A 129 -34.69 -39.37 REMARK 500 CYS A 178 -153.69 -99.26 REMARK 500 LYS A 209 54.75 -91.79 REMARK 500 ASN A 294 -168.09 -127.70 REMARK 500 ARG A 333 31.49 -97.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 897 DISTANCE = 5.83 ANGSTROMS 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 39.6 REMARK 620 3 HOH A 631 O 42.9 3.7 REMARK 620 4 HOH A 708 O 39.9 3.6 3.5 REMARK 620 5 HOH A 768 O 41.9 2.2 2.0 4.0 REMARK 620 6 HOH A 807 O 41.8 4.4 2.3 2.0 3.7 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 91.9 REMARK 620 3 VAL A 65 O 92.5 95.2 REMARK 620 4 HOH A 776 O 89.9 82.2 176.5 REMARK 620 5 DC D 3 OP1 175.8 91.8 89.2 88.5 REMARK 620 6 HOH D 114 O 90.9 175.1 88.8 93.7 85.3 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 93.5 REMARK 620 3 ILE A 106 O 92.8 87.7 REMARK 620 4 HOH A 790 O 83.4 94.7 175.6 REMARK 620 5 DG P 9 OP1 166.5 96.8 96.2 87.2 REMARK 620 6 HOH P 120 O 79.6 172.8 90.3 86.8 90.3 REMARK 620 N 1 2 3 4 5 DBREF 9Y16 A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 9Y16 T 1 16 PDB 9Y16 9Y16 1 16 DBREF 9Y16 P 1 10 PDB 9Y16 9Y16 1 10 DBREF 9Y16 D 1 5 PDB 9Y16 9Y16 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 DG DG DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DC SEQRES 1 D 5 DG DT DC DG DG HET NA A 401 1 HET NA A 402 1 HET 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 *556(H2 O) HELIX 1 AA1 GLN A 8 VAL A 29 1 22 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 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 GLY A 274 1 14 HELIX 16 AB7 SER A 275 LYS A 289 1 15 HELIX 17 AB8 SER A 315 ILE A 323 1 9 HELIX 18 AB9 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 2.40 LINK O LYS A 60 NA NA A 401 1555 1555 2.29 LINK O LEU A 62 NA NA A 401 1555 1555 2.50 LINK O VAL A 65 NA NA A 401 1555 1555 2.31 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 2.37 LINK OG SER A 171 NA NA A 403 1555 1555 2.26 LINK NA NA A 401 O HOH A 776 1555 1555 2.43 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.72 LINK NA NA A 401 O HOH D 114 1555 1555 2.40 LINK NA NA A 402 O HOH A 790 1555 1555 2.54 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.38 LINK NA NA A 402 O HOH P 120 1555 1555 2.52 LINK NA NA A 403 O HOH A 631 1555 1555 2.45 LINK NA NA A 403 O HOH A 708 1555 1555 2.34 LINK NA NA A 403 O HOH A 768 1555 1455 2.42 LINK NA NA A 403 O HOH A 807 1555 1455 2.46 CISPEP 1 GLY A 274 SER A 275 0 3.40 CRYST1 54.088 78.488 54.699 90.00 104.88 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 0.018488 0.000000 0.004912 0.00000 SCALE2 0.000000 0.012741 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018916 0.00000 CONECT 404 3235 CONECT 422 3235 CONECT 441 3235 CONECT 729 3236 CONECT 747 3236 CONECT 764 3236 CONECT 1311 3237 CONECT 3068 3236 CONECT 3172 3235 CONECT 3235 404 422 441 3172 CONECT 3235 3514 3768 CONECT 3236 729 747 764 3068 CONECT 3236 3528 3727 CONECT 3237 1311 3369 3446 CONECT 3369 3237 CONECT 3446 3237 CONECT 3514 3235 CONECT 3528 3236 CONECT 3727 3236 CONECT 3768 3235 MASTER 487 0 4 18 9 0 0 6 3748 4 20 30 END