HEADER REPLICATION 29-AUG-25 9Y1J TITLE S180R HUMAN DNA POLYMERASE BETA, TERNARY COMPLEX DT:DAMPCPP 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 9Y1J 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. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 118749 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.920 REMARK 3 FREE R VALUE TEST SET COUNT : 11784 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 42.7100 - 4.8200 0.99 3566 391 0.1365 0.1586 REMARK 3 2 4.8100 - 3.8200 1.00 3607 384 0.1142 0.1358 REMARK 3 3 3.8200 - 3.3400 1.00 3566 369 0.1214 0.1592 REMARK 3 4 3.3400 - 3.0300 1.00 3583 387 0.1382 0.1597 REMARK 3 5 3.0300 - 2.8200 1.00 3559 418 0.1496 0.1781 REMARK 3 6 2.8200 - 2.6500 1.00 3586 374 0.1538 0.1909 REMARK 3 7 2.6500 - 2.5200 1.00 3631 380 0.1541 0.2018 REMARK 3 8 2.5200 - 2.4100 1.00 3562 402 0.1467 0.1771 REMARK 3 9 2.4100 - 2.3200 1.00 3560 437 0.1505 0.1866 REMARK 3 10 2.3200 - 2.2400 1.00 3602 394 0.1530 0.1789 REMARK 3 11 2.2400 - 2.1700 1.00 3615 423 0.1506 0.1921 REMARK 3 12 2.1700 - 2.1000 1.00 3532 398 0.1538 0.1819 REMARK 3 13 2.1000 - 2.0500 1.00 3549 419 0.1510 0.2042 REMARK 3 14 2.0500 - 2.0000 1.00 3657 379 0.1543 0.1920 REMARK 3 15 2.0000 - 1.9500 1.00 3611 330 0.1534 0.1807 REMARK 3 16 1.9500 - 1.9100 1.00 3590 419 0.1597 0.2093 REMARK 3 17 1.9100 - 1.8700 1.00 3576 398 0.1595 0.2002 REMARK 3 18 1.8700 - 1.8400 1.00 3626 399 0.1631 0.2078 REMARK 3 19 1.8400 - 1.8000 1.00 3601 378 0.1764 0.2013 REMARK 3 20 1.8000 - 1.7700 1.00 3577 400 0.1801 0.2259 REMARK 3 21 1.7700 - 1.7500 1.00 3555 370 0.1713 0.2205 REMARK 3 22 1.7500 - 1.7200 1.00 3688 380 0.1691 0.1931 REMARK 3 23 1.7200 - 1.6900 1.00 3527 416 0.1698 0.1981 REMARK 3 24 1.6900 - 1.6700 1.00 3644 393 0.1641 0.1912 REMARK 3 25 1.6700 - 1.6500 1.00 3515 383 0.1623 0.2039 REMARK 3 26 1.6500 - 1.6300 1.00 3678 368 0.1822 0.2063 REMARK 3 27 1.6300 - 1.6100 0.99 3521 415 0.1984 0.2360 REMARK 3 28 1.6100 - 1.5900 0.98 3428 407 0.2028 0.2660 REMARK 3 29 1.5900 - 1.5700 0.95 3410 423 0.2242 0.2413 REMARK 3 30 1.5700 - 1.5500 0.90 3243 350 0.2356 0.2482 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.30 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 : 0.012 3521 REMARK 3 ANGLE : 1.306 4900 REMARK 3 CHIRALITY : 0.074 536 REMARK 3 PLANARITY : 0.012 523 REMARK 3 DIHEDRAL : 19.640 1425 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): 25.4785 4.4804 -2.7397 REMARK 3 T TENSOR REMARK 3 T11: 0.2383 T22: 0.3437 REMARK 3 T33: 0.2267 T12: -0.0194 REMARK 3 T13: 0.1360 T23: 0.0932 REMARK 3 L TENSOR REMARK 3 L11: 0.2509 L22: 0.5098 REMARK 3 L33: 0.7785 L12: -0.1943 REMARK 3 L13: 0.1317 L23: 0.4299 REMARK 3 S TENSOR REMARK 3 S11: 0.2097 S12: 0.4616 S13: 0.5358 REMARK 3 S21: -0.7210 S22: -0.0657 S23: -0.4362 REMARK 3 S31: -0.2204 S32: 0.3683 S33: -0.0916 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): 12.4606 16.0837 14.6080 REMARK 3 T TENSOR REMARK 3 T11: 0.1161 T22: 0.0866 REMARK 3 T33: 0.1137 T12: -0.0416 REMARK 3 T13: 0.0206 T23: -0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.1259 L22: 0.2685 REMARK 3 L33: 0.1073 L12: -0.1833 REMARK 3 L13: -0.0395 L23: 0.0657 REMARK 3 S TENSOR REMARK 3 S11: -0.0256 S12: 0.0243 S13: 0.1468 REMARK 3 S21: -0.0231 S22: -0.0309 S23: -0.1421 REMARK 3 S31: -0.0650 S32: 0.0277 S33: -0.2728 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 12:90 REMARK 3 ORIGIN FOR THE GROUP (A): 22.3921 -8.1060 10.4287 REMARK 3 T TENSOR REMARK 3 T11: 0.0956 T22: 0.1108 REMARK 3 T33: 0.0894 T12: 0.0237 REMARK 3 T13: -0.0055 T23: -0.0137 REMARK 3 L TENSOR REMARK 3 L11: 0.5153 L22: 0.7235 REMARK 3 L33: 0.7997 L12: -0.1286 REMARK 3 L13: 0.2044 L23: -0.0420 REMARK 3 S TENSOR REMARK 3 S11: 0.0456 S12: 0.0124 S13: 0.0067 REMARK 3 S21: -0.0621 S22: -0.0283 S23: -0.1016 REMARK 3 S31: 0.1947 S32: 0.1666 S33: -0.0094 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 91:150 REMARK 3 ORIGIN FOR THE GROUP (A): 17.0910 7.3787 30.5069 REMARK 3 T TENSOR REMARK 3 T11: 0.0635 T22: 0.1231 REMARK 3 T33: 0.1162 T12: -0.0033 REMARK 3 T13: -0.0203 T23: -0.0109 REMARK 3 L TENSOR REMARK 3 L11: 0.4354 L22: 0.2979 REMARK 3 L33: 0.7010 L12: 0.0218 REMARK 3 L13: -0.2415 L23: -0.1612 REMARK 3 S TENSOR REMARK 3 S11: 0.0635 S12: -0.1977 S13: -0.0731 REMARK 3 S21: 0.0680 S22: -0.0419 S23: -0.1505 REMARK 3 S31: -0.0581 S32: 0.2040 S33: -0.0071 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND RESID 151:260 REMARK 3 ORIGIN FOR THE GROUP (A): -6.3942 10.9062 20.1037 REMARK 3 T TENSOR REMARK 3 T11: 0.0386 T22: 0.0884 REMARK 3 T33: 0.0764 T12: 0.0183 REMARK 3 T13: 0.0062 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.8271 L22: 0.6982 REMARK 3 L33: 1.1168 L12: 0.0178 REMARK 3 L13: 0.0738 L23: 0.3678 REMARK 3 S TENSOR REMARK 3 S11: -0.0104 S12: -0.0627 S13: 0.0341 REMARK 3 S21: 0.0326 S22: -0.0102 S23: 0.1037 REMARK 3 S31: -0.0654 S32: -0.2184 S33: -0.0302 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND RESID 261:335 REMARK 3 ORIGIN FOR THE GROUP (A): 3.0480 8.4689 -1.6053 REMARK 3 T TENSOR REMARK 3 T11: 0.1496 T22: 0.1174 REMARK 3 T33: 0.0702 T12: 0.0030 REMARK 3 T13: 0.0060 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 0.6554 L22: 0.6955 REMARK 3 L33: 0.6807 L12: -0.2154 REMARK 3 L13: -0.0415 L23: 0.1812 REMARK 3 S TENSOR REMARK 3 S11: 0.0137 S12: 0.2119 S13: -0.0116 REMARK 3 S21: -0.3751 S22: -0.0115 S23: -0.0240 REMARK 3 S31: -0.0351 S32: 0.0071 S33: 0.0018 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): 18.7542 30.5151 17.7339 REMARK 3 T TENSOR REMARK 3 T11: 0.2173 T22: -0.1612 REMARK 3 T33: 0.4609 T12: -0.1928 REMARK 3 T13: -0.0158 T23: -0.1159 REMARK 3 L TENSOR REMARK 3 L11: 0.1837 L22: 1.0977 REMARK 3 L33: 0.4816 L12: -0.0973 REMARK 3 L13: 0.1576 L23: -0.4985 REMARK 3 S TENSOR REMARK 3 S11: -0.2165 S12: -0.2539 S13: 0.2048 REMARK 3 S21: -0.2422 S22: -0.3168 S23: -0.5528 REMARK 3 S31: 0.0335 S32: -0.0687 S33: -1.1216 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 9Y1J 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_1000299671. 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 : DIALS 3.8 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 118749 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 44.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.48800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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 WITH 1 MM DNTP REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 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 39.58900 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: 5120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20070 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 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 793 O HOH T 162 1.94 REMARK 500 O HOH A 503 O HOH A 616 1.96 REMARK 500 O HOH A 676 O HOH A 886 1.97 REMARK 500 O HOH A 869 O HOH A 960 2.01 REMARK 500 O HOH A 524 O HOH A 898 2.02 REMARK 500 O HOH A 502 O HOH A 654 2.02 REMARK 500 O HOH A 720 O HOH A 950 2.04 REMARK 500 O HOH A 632 O HOH A 949 2.07 REMARK 500 O HOH T 101 O HOH T 171 2.08 REMARK 500 OE1 GLU A 288 O HOH A 501 2.09 REMARK 500 O HOH A 539 O HOH A 615 2.09 REMARK 500 O HOH A 958 O HOH P 103 2.09 REMARK 500 O HOH A 677 O HOH A 946 2.10 REMARK 500 O HOH A 649 O HOH A 874 2.10 REMARK 500 NH2 ARG A 40 O HOH A 502 2.10 REMARK 500 O HOH A 882 O HOH A 885 2.12 REMARK 500 OP2 DC P 2 O HOH P 101 2.13 REMARK 500 O HOH A 879 O HOH A 946 2.14 REMARK 500 O HOH P 144 O HOH P 148 2.15 REMARK 500 O5' DT T 6 O HOH T 101 2.15 REMARK 500 O HOH A 670 O HOH A 816 2.15 REMARK 500 O HOH T 113 O HOH T 162 2.16 REMARK 500 O HOH A 886 O HOH A 995 2.16 REMARK 500 O HOH A 511 O HOH A 916 2.16 REMARK 500 O HOH A 564 O HOH A 946 2.16 REMARK 500 O HOH A 882 O HOH A 925 2.16 REMARK 500 O HOH A 695 O HOH A 845 2.17 REMARK 500 O HOH A 829 O HOH A 870 2.18 REMARK 500 OP2 DG P 7 O HOH P 102 2.18 REMARK 500 O HOH A 837 O HOH A 907 2.19 REMARK 500 O HOH T 101 O HOH T 109 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 696 O HOH A 979 1556 2.17 REMARK 500 O HOH A 623 O HOH T 170 1556 2.18 REMARK 500 O HOH A 670 O HOH T 179 2646 2.19 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 DC T 2 O3' DC T 2 C3' -0.042 REMARK 500 DG P 9 O3' DG P 9 C3' -0.056 REMARK 500 DG D 1 P DG D 1 OP3 -0.108 REMARK 500 DC D 3 O3' DC D 3 C3' -0.051 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 P 7 O5' - P - OP2 ANGL. DEV. = -6.3 DEGREES REMARK 500 DG D 4 O4' - C1' - N9 ANGL. DEV. = -4.3 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 -146.16 -114.34 REMARK 500 ASN A 294 -168.40 -128.97 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 A1009 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH T 187 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH T 188 DISTANCE = 6.24 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 95.6 REMARK 620 3 VAL A 65 O 91.8 94.1 REMARK 620 4 HOH A 810 O 88.7 83.2 177.2 REMARK 620 5 DC D 3 OP1 172.1 92.2 88.5 91.4 REMARK 620 6 HOH D 109 O 89.5 174.3 88.4 94.3 82.7 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 95.8 REMARK 620 3 ILE A 106 O 96.5 88.8 REMARK 620 4 HOH A 863 O 81.7 91.0 178.1 REMARK 620 5 DG P 9 OP1 163.6 95.4 95.8 86.1 REMARK 620 6 HOH P 112 O 78.8 174.5 90.7 89.3 90.1 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 109.1 REMARK 620 3 ASP A 256 OD2 95.6 96.1 REMARK 620 4 F2A A 405 O1A 95.3 88.5 166.1 REMARK 620 5 HOH A 611 O 80.2 167.1 91.8 81.6 REMARK 620 6 DC P 10 O3' 162.7 86.9 75.6 91.6 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 96.7 REMARK 620 3 F2A A 405 O2B 169.5 91.5 REMARK 620 4 F2A A 405 O1A 96.1 92.3 90.1 REMARK 620 5 F2A A 405 O3G 85.0 177.9 86.7 88.6 REMARK 620 6 HOH A 709 O 86.6 90.6 86.7 175.8 88.4 REMARK 620 N 1 2 3 4 5 DBREF 9Y1J A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 9Y1J T 1 16 PDB 9Y1J 9Y1J 1 16 DBREF 9Y1J P 1 10 PDB 9Y1J 9Y1J 1 10 DBREF 9Y1J D 1 5 PDB 9Y1J 9Y1J 1 5 SEQADV 9Y1J ARG A 180 UNP P06746 SER 180 ENGINEERED MUTATION SEQRES 1 A 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY ARG PHE ARG SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU SEQRES 1 T 16 DC DC DG DA DC DT DG DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DC SEQRES 1 D 5 DG DT DC DG DG HET NA A 401 1 HET NA A 402 1 HET MG A 403 1 HET MG A 404 1 HET F2A A 405 30 HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETNAM F2A 2'-DEOXY-5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 2 F2A PHOSPHORYL]METHYL}PHOSPHORYL]ADENOSINE FORMUL 5 NA 2(NA 1+) FORMUL 7 MG 2(MG 2+) FORMUL 9 F2A C11 H18 N5 O11 P3 FORMUL 10 HOH *674(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 GLU A 147 1 6 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 GLY A 237 O ILE A 255 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 2.30 LINK O LEU A 62 NA NA A 401 1555 1555 2.44 LINK O VAL A 65 NA NA A 401 1555 1555 2.35 LINK O THR A 101 NA NA A 402 1555 1555 2.29 LINK O VAL A 103 NA NA A 402 1555 1555 2.49 LINK O ILE A 106 NA NA A 402 1555 1555 2.36 LINK OD2 ASP A 190 MG MG A 403 1555 1555 2.05 LINK OD1 ASP A 190 MG MG A 404 1555 1555 2.00 LINK OD1 ASP A 192 MG MG A 403 1555 1555 2.11 LINK OD2 ASP A 192 MG MG A 404 1555 1555 1.99 LINK OD2 ASP A 256 MG MG A 403 1555 1555 2.09 LINK NA NA A 401 O HOH A 810 1555 1555 2.43 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.64 LINK NA NA A 401 O HOH D 109 1555 1555 2.53 LINK NA NA A 402 O HOH A 863 1555 1555 2.48 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.44 LINK NA NA A 402 O HOH P 112 1555 1555 2.52 LINK MG MG A 403 O1A F2A A 405 1555 1555 2.25 LINK MG MG A 403 O HOH A 611 1555 1555 2.13 LINK MG MG A 403 O3' DC P 10 1555 1555 2.29 LINK MG MG A 404 O2B F2A A 405 1555 1555 2.05 LINK MG MG A 404 O1A F2A A 405 1555 1555 2.13 LINK MG MG A 404 O3G F2A A 405 1555 1555 2.13 LINK MG MG A 404 O HOH A 709 1555 1555 2.14 CISPEP 1 GLY A 274 SER A 275 0 1.18 CRYST1 50.772 79.178 55.525 90.00 107.57 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 0.019696 0.000000 0.006237 0.00000 SCALE2 0.000000 0.012630 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018891 0.00000 CONECT 396 3353 CONECT 414 3353 CONECT 433 3353 CONECT 733 3354 CONECT 751 3354 CONECT 771 3354 CONECT 1485 3356 CONECT 1486 3355 CONECT 1506 3355 CONECT 1507 3356 CONECT 2048 3355 CONECT 3205 3354 CONECT 3234 3355 CONECT 3290 3353 CONECT 3353 396 414 433 3290 CONECT 3353 3696 4041 CONECT 3354 733 751 771 3205 CONECT 3354 3749 3995 CONECT 3355 1486 1506 2048 3234 CONECT 3355 3358 3497 CONECT 3356 1485 1507 3358 3364 CONECT 3356 3369 3595 CONECT 3357 3358 3359 3360 3361 CONECT 3358 3355 3356 3357 CONECT 3359 3357 CONECT 3360 3357 3362 CONECT 3361 3357 3370 CONECT 3362 3360 3363 3364 3365 CONECT 3363 3362 CONECT 3364 3356 3362 CONECT 3365 3362 3366 CONECT 3366 3365 3367 3368 3369 CONECT 3367 3366 CONECT 3368 3366 CONECT 3369 3356 3366 CONECT 3370 3361 3371 CONECT 3371 3370 3372 3385 CONECT 3372 3371 3373 CONECT 3373 3372 3374 3384 CONECT 3374 3373 3375 3383 CONECT 3375 3374 3376 3381 CONECT 3376 3375 3377 CONECT 3377 3376 3378 CONECT 3378 3377 3379 CONECT 3379 3378 3380 3381 CONECT 3380 3379 CONECT 3381 3375 3379 3382 CONECT 3382 3381 3383 CONECT 3383 3374 3382 CONECT 3384 3373 3385 CONECT 3385 3371 3384 3386 CONECT 3386 3385 CONECT 3497 3355 CONECT 3595 3356 CONECT 3696 3353 CONECT 3749 3354 CONECT 3995 3354 CONECT 4041 3353 MASTER 527 0 5 19 9 0 0 6 3957 4 58 30 END