HEADER REPLICATION 29-AUG-25 9Y1K TITLE S180R HUMAN DNA POLYMERASE BETA, TERNARY COMPLEX DC:DGMPCPP 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 9Y1K 0 JRNL AUTH D.L.SAWYER,B.E.ECKENROTH,C.CHAVIRA,K.ALNAJJAR,J.P.HANLEY, JRNL AUTH 2 J.A.DRAGON,S.DOUBLIE,J.B.SWEASY JRNL TITL THE S180R HUMAN GERMLINE VARIANT OF DNA POLYMERASE BETA IS A JRNL TITL 2 LOW FIDELITY ENZYME WITH REDUCED FLEXIBILITY OF THE FINGERS JRNL TITL 3 DOMAIN. JRNL REF BIOCHEMISTRY 2026 JRNL REFN ISSN 0006-2960 JRNL PMID 41524291 JRNL DOI 10.1021/ACS.BIOCHEM.5C00628 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 88705 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.140 REMARK 3 FREE R VALUE TEST SET COUNT : 8995 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 44.1800 - 5.2800 0.97 2676 294 0.1314 0.1512 REMARK 3 2 5.2800 - 4.1900 0.98 2656 299 0.1187 0.1625 REMARK 3 3 4.1900 - 3.6600 0.97 2708 263 0.1251 0.1689 REMARK 3 4 3.6600 - 3.3300 0.98 2743 276 0.1307 0.1739 REMARK 3 5 3.3300 - 3.0900 0.98 2676 282 0.1441 0.1814 REMARK 3 6 3.0900 - 2.9100 0.98 2692 300 0.1604 0.1916 REMARK 3 7 2.9100 - 2.7600 0.98 2651 333 0.1638 0.2244 REMARK 3 8 2.7600 - 2.6400 0.97 2702 273 0.1739 0.2303 REMARK 3 9 2.6400 - 2.5400 0.98 2695 284 0.1691 0.2358 REMARK 3 10 2.5400 - 2.4500 0.98 2705 307 0.1644 0.2099 REMARK 3 11 2.4500 - 2.3800 0.98 2644 306 0.1710 0.2403 REMARK 3 12 2.3800 - 2.3100 0.98 2645 311 0.1790 0.2278 REMARK 3 13 2.3100 - 2.2500 0.98 2712 301 0.1918 0.2250 REMARK 3 14 2.2500 - 2.1900 0.98 2671 318 0.2033 0.2519 REMARK 3 15 2.1900 - 2.1400 0.98 2690 282 0.1867 0.2111 REMARK 3 16 2.1400 - 2.1000 0.98 2649 309 0.1892 0.2472 REMARK 3 17 2.1000 - 2.0500 0.98 2659 330 0.2104 0.2770 REMARK 3 18 2.0500 - 2.0200 0.97 2692 277 0.2215 0.2621 REMARK 3 19 2.0200 - 1.9800 0.98 2730 290 0.2168 0.2584 REMARK 3 20 1.9800 - 1.9500 0.98 2674 287 0.2319 0.2604 REMARK 3 21 1.9500 - 1.9100 0.98 2688 293 0.2721 0.3063 REMARK 3 22 1.9100 - 1.8900 0.97 2653 306 0.2931 0.3041 REMARK 3 23 1.8900 - 1.8600 0.98 2651 333 0.2936 0.3030 REMARK 3 24 1.8600 - 1.8300 0.97 2677 316 0.2903 0.3066 REMARK 3 25 1.8300 - 1.8100 0.97 2602 330 0.2781 0.3008 REMARK 3 26 1.8100 - 1.7800 0.97 2678 273 0.2818 0.3211 REMARK 3 27 1.7800 - 1.7600 0.96 2659 302 0.2967 0.3081 REMARK 3 28 1.7600 - 1.7400 0.94 2527 309 0.2931 0.3301 REMARK 3 29 1.7400 - 1.7200 0.93 2567 318 0.3150 0.3519 REMARK 3 30 1.7200 - 1.7000 0.88 2338 293 0.3094 0.3483 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.30 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 3464 REMARK 3 ANGLE : 0.920 4812 REMARK 3 CHIRALITY : 0.052 525 REMARK 3 PLANARITY : 0.008 503 REMARK 3 DIHEDRAL : 20.434 1375 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ((CHAIN D AND RESID 1:5) OR (CHAIN T AND RESID 1:6)) REMARK 3 ORIGIN FOR THE GROUP (A): 24.5218 4.6995 -1.9881 REMARK 3 T TENSOR REMARK 3 T11: 0.5001 T22: 0.5749 REMARK 3 T33: 0.4322 T12: -0.0188 REMARK 3 T13: 0.2059 T23: 0.0805 REMARK 3 L TENSOR REMARK 3 L11: 0.0181 L22: 0.2330 REMARK 3 L33: 0.3281 L12: -0.0456 REMARK 3 L13: -0.0326 L23: 0.3032 REMARK 3 S TENSOR REMARK 3 S11: 0.3821 S12: 0.3976 S13: 0.8238 REMARK 3 S21: -1.0543 S22: -0.0210 S23: -0.6967 REMARK 3 S31: -0.3158 S32: 0.3334 S33: 0.0314 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): 12.5322 16.0680 14.4762 REMARK 3 T TENSOR REMARK 3 T11: 0.2211 T22: 0.1717 REMARK 3 T33: 0.2193 T12: -0.0557 REMARK 3 T13: 0.0206 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 0.3239 L22: 0.5056 REMARK 3 L33: 0.5434 L12: -0.4218 REMARK 3 L13: 0.0235 L23: -0.0050 REMARK 3 S TENSOR REMARK 3 S11: -0.0003 S12: 0.0507 S13: 0.1210 REMARK 3 S21: -0.0796 S22: -0.0529 S23: -0.2838 REMARK 3 S31: -0.0265 S32: -0.0564 S33: 0.0002 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 12:90 REMARK 3 ORIGIN FOR THE GROUP (A): 22.2023 -8.6814 10.2165 REMARK 3 T TENSOR REMARK 3 T11: 0.1808 T22: 0.2272 REMARK 3 T33: 0.1774 T12: 0.0442 REMARK 3 T13: -0.0026 T23: -0.0214 REMARK 3 L TENSOR REMARK 3 L11: 1.4644 L22: 2.1399 REMARK 3 L33: 1.2757 L12: 0.0908 REMARK 3 L13: 0.3811 L23: 0.0417 REMARK 3 S TENSOR REMARK 3 S11: 0.0621 S12: 0.0884 S13: 0.0158 REMARK 3 S21: -0.1542 S22: -0.0365 S23: -0.1664 REMARK 3 S31: 0.2064 S32: 0.2463 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 91:150 REMARK 3 ORIGIN FOR THE GROUP (A): 17.3583 6.9152 30.3607 REMARK 3 T TENSOR REMARK 3 T11: 0.1669 T22: 0.2267 REMARK 3 T33: 0.1978 T12: 0.0017 REMARK 3 T13: -0.0352 T23: -0.0192 REMARK 3 L TENSOR REMARK 3 L11: 1.3302 L22: 0.9835 REMARK 3 L33: 1.4771 L12: 0.1228 REMARK 3 L13: -0.1461 L23: -0.3383 REMARK 3 S TENSOR REMARK 3 S11: -0.0020 S12: -0.2619 S13: -0.0548 REMARK 3 S21: 0.1192 S22: 0.0054 S23: -0.1777 REMARK 3 S31: -0.0770 S32: 0.2549 S33: -0.0001 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND RESID 151:260 REMARK 3 ORIGIN FOR THE GROUP (A): -6.2036 10.5165 20.2445 REMARK 3 T TENSOR REMARK 3 T11: 0.1072 T22: 0.1803 REMARK 3 T33: 0.1697 T12: 0.0210 REMARK 3 T13: 0.0027 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 1.1774 L22: 1.3987 REMARK 3 L33: 2.6523 L12: -0.0542 REMARK 3 L13: 0.0917 L23: -0.0989 REMARK 3 S TENSOR REMARK 3 S11: -0.0258 S12: -0.0663 S13: 0.0219 REMARK 3 S21: 0.0151 S22: 0.0281 S23: 0.1209 REMARK 3 S31: -0.1415 S32: -0.2983 S33: 0.0004 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND RESID 261:335 REMARK 3 ORIGIN FOR THE GROUP (A): 3.0535 8.3852 -1.8080 REMARK 3 T TENSOR REMARK 3 T11: 0.2574 T22: 0.2174 REMARK 3 T33: 0.1624 T12: -0.0139 REMARK 3 T13: 0.0101 T23: -0.0085 REMARK 3 L TENSOR REMARK 3 L11: 1.4693 L22: 1.5034 REMARK 3 L33: 1.9003 L12: -0.3660 REMARK 3 L13: -0.2769 L23: 0.3824 REMARK 3 S TENSOR REMARK 3 S11: 0.0374 S12: 0.2519 S13: -0.0128 REMARK 3 S21: -0.4505 S22: 0.0007 S23: -0.0667 REMARK 3 S31: -0.0748 S32: 0.0076 S33: 0.0020 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): 18.7401 30.5534 17.9065 REMARK 3 T TENSOR REMARK 3 T11: 0.3277 T22: 0.2161 REMARK 3 T33: 0.5496 T12: -0.0669 REMARK 3 T13: 0.0221 T23: -0.0596 REMARK 3 L TENSOR REMARK 3 L11: 0.3054 L22: 0.4285 REMARK 3 L33: 1.2384 L12: -0.1177 REMARK 3 L13: -0.1166 L23: -0.6137 REMARK 3 S TENSOR REMARK 3 S11: -0.0494 S12: -0.2872 S13: 0.1957 REMARK 3 S21: -0.2925 S22: -0.6483 S23: -0.9238 REMARK 3 S31: 0.0262 S32: -0.0053 S33: -0.1344 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 9Y1K 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_1000299672. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.4.0 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 88705 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 48.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.17700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 1.91800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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 WITH 1 MM DNTP REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 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 40.02950 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: 5040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 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 GLU A 9 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 VAL A 303 CG1 CG2 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 760 O HOH A 821 2.09 REMARK 500 O HOH A 627 O HOH A 742 2.10 REMARK 500 O HOH A 743 O HOH A 839 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 596 O HOH A 820 1556 2.08 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 -0.126 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 D 5 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 CYS A 178 -152.18 -117.08 REMARK 500 ASN A 294 -169.51 -125.48 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 P 134 DISTANCE = 6.70 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 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 91.7 REMARK 620 3 VAL A 65 O 92.2 94.5 REMARK 620 4 HOH A 739 O 87.6 84.3 178.8 REMARK 620 5 DC D 3 OP1 170.8 97.5 87.6 92.8 REMARK 620 6 HOH D 105 O 93.1 173.6 89.6 91.6 77.7 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 94.7 REMARK 620 3 ILE A 106 O 95.5 89.8 REMARK 620 4 HOH A 787 O 84.5 87.7 177.6 REMARK 620 5 DG P 9 OP1 165.3 95.1 95.4 85.1 REMARK 620 6 HOH P 112 O 79.1 173.1 93.8 88.6 90.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD2 REMARK 620 2 ASP A 192 OD1 104.2 REMARK 620 3 ASP A 256 OD2 90.4 98.2 REMARK 620 4 1GC A 405 O2A 95.9 90.1 168.1 REMARK 620 5 HOH A 521 O 83.0 166.5 93.0 77.7 REMARK 620 6 DC P 10 O3' 163.1 89.9 78.2 93.4 85.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 93.4 REMARK 620 3 1GC A 405 O2A 99.7 92.6 REMARK 620 4 1GC A 405 O2B 167.3 92.3 91.5 REMARK 620 5 1GC A 405 O1G 87.9 176.3 90.6 85.8 REMARK 620 6 HOH A 585 O 81.0 88.4 178.7 87.8 88.3 REMARK 620 N 1 2 3 4 5 DBREF 9Y1K A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 9Y1K T 1 16 PDB 9Y1K 9Y1K 1 16 DBREF 9Y1K P 1 10 PDB 9Y1K 9Y1K 1 10 DBREF 9Y1K D 1 5 PDB 9Y1K 9Y1K 1 5 SEQADV 9Y1K 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 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 MG A 403 1 HET MG A 404 1 HET 1GC A 405 31 HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETNAM 1GC 2'-DEOXY-5'-O-[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 2 1GC PHOSPHORYL]METHYL}PHOSPHORYL]GUANOSINE FORMUL 5 NA 2(NA 1+) FORMUL 7 MG 2(MG 2+) FORMUL 9 1GC C11 H18 N5 O12 P3 FORMUL 10 HOH *465(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 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 LEU A 228 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 2.49 LINK O LEU A 62 NA NA A 401 1555 1555 2.35 LINK O VAL A 65 NA NA A 401 1555 1555 2.30 LINK O THR A 101 NA NA A 402 1555 1555 2.30 LINK O VAL A 103 NA NA A 402 1555 1555 2.45 LINK O ILE A 106 NA NA A 402 1555 1555 2.33 LINK OD2 ASP A 190 MG MG A 403 1555 1555 2.05 LINK OD1 ASP A 190 MG MG A 404 1555 1555 2.04 LINK OD1 ASP A 192 MG MG A 403 1555 1555 1.98 LINK OD2 ASP A 192 MG MG A 404 1555 1555 2.04 LINK OD2 ASP A 256 MG MG A 403 1555 1555 2.03 LINK NA NA A 401 O HOH A 739 1555 1555 2.49 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.60 LINK NA NA A 401 O HOH D 105 1555 1555 2.92 LINK NA NA A 402 O HOH A 787 1555 1555 2.66 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.57 LINK NA NA A 402 O HOH P 112 1555 1555 2.36 LINK MG MG A 403 O2A 1GC A 405 1555 1555 2.26 LINK MG MG A 403 O HOH A 521 1555 1555 2.17 LINK MG MG A 403 O3' DC P 10 1555 1555 2.29 LINK MG MG A 404 O2A 1GC A 405 1555 1555 2.12 LINK MG MG A 404 O2B 1GC A 405 1555 1555 2.03 LINK MG MG A 404 O1G 1GC A 405 1555 1555 2.11 LINK MG MG A 404 O HOH A 585 1555 1555 2.11 CISPEP 1 GLY A 274 SER A 275 0 -2.75 CRYST1 50.617 80.059 55.529 90.00 107.46 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 0.019756 0.000000 0.006214 0.00000 SCALE2 0.000000 0.012491 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018878 0.00000 CONECT 396 3305 CONECT 414 3305 CONECT 433 3305 CONECT 718 3306 CONECT 736 3306 CONECT 753 3306 CONECT 1440 3308 CONECT 1441 3307 CONECT 1456 3307 CONECT 1457 3308 CONECT 1983 3307 CONECT 3157 3306 CONECT 3186 3307 CONECT 3242 3305 CONECT 3305 396 414 433 3242 CONECT 3305 3578 3794 CONECT 3306 718 736 753 3157 CONECT 3306 3626 3767 CONECT 3307 1441 1456 1983 3186 CONECT 3307 3328 3360 CONECT 3308 1440 1457 3326 3328 CONECT 3308 3329 3424 CONECT 3309 3310 3315 CONECT 3310 3309 3311 3312 CONECT 3311 3310 CONECT 3312 3310 3313 CONECT 3313 3312 3314 3319 CONECT 3314 3313 3315 3317 CONECT 3315 3309 3314 3316 CONECT 3316 3315 CONECT 3317 3314 3318 CONECT 3318 3317 3319 CONECT 3319 3313 3318 3323 CONECT 3320 3324 3328 3333 3339 CONECT 3321 3325 3329 3333 3334 CONECT 3322 3326 3330 3334 3335 CONECT 3323 3319 3327 3337 CONECT 3324 3320 CONECT 3325 3321 CONECT 3326 3308 3322 CONECT 3327 3323 3331 CONECT 3328 3307 3308 3320 CONECT 3329 3308 3321 CONECT 3330 3322 CONECT 3331 3327 3332 3336 CONECT 3332 3331 CONECT 3333 3320 3321 CONECT 3334 3321 3322 CONECT 3335 3322 CONECT 3336 3331 3337 3338 CONECT 3337 3323 3336 CONECT 3338 3336 3339 CONECT 3339 3320 3338 CONECT 3360 3307 CONECT 3424 3308 CONECT 3578 3305 CONECT 3626 3306 CONECT 3767 3306 CONECT 3794 3305 MASTER 498 0 5 19 9 0 0 6 3746 4 59 30 END