HEADER REPLICATION, HYDROLASE/DNA 29-AUG-25 9Y19 TITLE WT HUMAN DNA POLYMERASE BETA, TERNARY COMPLEX DA:DUMPNPP 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 9Y19 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 3 NUMBER OF REFLECTIONS : 57170 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) : 0.148 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 5659 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 24.9900 - 5.8800 0.97 1908 205 0.1286 0.1354 REMARK 3 2 5.8800 - 4.6800 0.98 1902 215 0.1262 0.1807 REMARK 3 3 4.6800 - 4.0900 0.98 1916 202 0.1123 0.1616 REMARK 3 4 4.0900 - 3.7200 0.98 1897 224 0.1143 0.1549 REMARK 3 5 3.7200 - 3.4500 0.98 1957 172 0.1279 0.1749 REMARK 3 6 3.4500 - 3.2500 0.98 1921 196 0.1274 0.1533 REMARK 3 7 3.2500 - 3.0800 0.98 1923 214 0.1421 0.1829 REMARK 3 8 3.0800 - 2.9500 0.98 1883 217 0.1511 0.2080 REMARK 3 9 2.9500 - 2.8400 0.97 1903 215 0.1528 0.1978 REMARK 3 10 2.8400 - 2.7400 0.98 1924 212 0.1560 0.2259 REMARK 3 11 2.7400 - 2.6500 0.95 1828 196 0.1591 0.2190 REMARK 3 12 2.6500 - 2.5800 0.92 1836 195 0.1549 0.2291 REMARK 3 13 2.5800 - 2.5100 0.90 1760 177 0.1510 0.2107 REMARK 3 14 2.5100 - 2.4500 0.89 1746 200 0.1528 0.1877 REMARK 3 15 2.4500 - 2.3900 0.88 1685 214 0.1566 0.2339 REMARK 3 16 2.3900 - 2.3400 0.87 1676 191 0.1654 0.2135 REMARK 3 17 2.3400 - 2.3000 0.85 1637 195 0.1588 0.2110 REMARK 3 18 2.3000 - 2.2500 0.84 1663 155 0.1598 0.1839 REMARK 3 19 2.2500 - 2.2100 0.84 1662 192 0.1618 0.2253 REMARK 3 20 2.2100 - 2.1700 0.83 1581 193 0.1674 0.2486 REMARK 3 21 2.1700 - 2.1400 0.83 1604 177 0.1661 0.2367 REMARK 3 22 2.1400 - 2.1100 0.81 1571 165 0.1675 0.2249 REMARK 3 23 2.1100 - 2.0800 0.77 1501 216 0.1767 0.2423 REMARK 3 24 2.0800 - 2.0500 0.77 1462 159 0.1829 0.2760 REMARK 3 25 2.0500 - 2.0200 0.79 1572 147 0.1911 0.1889 REMARK 3 26 2.0200 - 1.9900 0.77 1519 157 0.1933 0.2537 REMARK 3 27 1.9900 - 1.9700 0.79 1565 148 0.1961 0.2394 REMARK 3 28 1.9700 - 1.9400 0.77 1509 165 0.2114 0.2777 REMARK 3 29 1.9400 - 1.9200 0.77 1467 197 0.2371 0.3080 REMARK 3 30 1.9200 - 1.9000 0.77 1533 148 0.2572 0.2938 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) : 19.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.40 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 : 0.011 3420 REMARK 3 ANGLE : 1.114 4746 REMARK 3 CHIRALITY : 0.062 520 REMARK 3 PLANARITY : 0.011 501 REMARK 3 DIHEDRAL : 19.895 1350 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): 22.4762 -8.5835 10.2370 REMARK 3 T TENSOR REMARK 3 T11: 0.1207 T22: 0.1468 REMARK 3 T33: 0.1259 T12: 0.0330 REMARK 3 T13: -0.0070 T23: -0.0271 REMARK 3 L TENSOR REMARK 3 L11: 0.8224 L22: 1.4748 REMARK 3 L33: 0.8261 L12: 0.0287 REMARK 3 L13: 0.3249 L23: 0.0881 REMARK 3 S TENSOR REMARK 3 S11: 0.0175 S12: 0.0216 S13: -0.0401 REMARK 3 S21: -0.0434 S22: 0.0317 S23: -0.1823 REMARK 3 S31: 0.1430 S32: 0.2078 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 91:150 REMARK 3 ORIGIN FOR THE GROUP (A): 17.4407 7.0370 30.3953 REMARK 3 T TENSOR REMARK 3 T11: 0.1191 T22: 0.2018 REMARK 3 T33: 0.1640 T12: 0.0153 REMARK 3 T13: -0.0284 T23: -0.0193 REMARK 3 L TENSOR REMARK 3 L11: 0.8574 L22: 0.6656 REMARK 3 L33: 0.8901 L12: 0.2224 REMARK 3 L13: -0.1684 L23: -0.0455 REMARK 3 S TENSOR REMARK 3 S11: -0.0163 S12: -0.4050 S13: -0.0498 REMARK 3 S21: 0.1491 S22: 0.0215 S23: -0.1594 REMARK 3 S31: -0.0084 S32: 0.2280 S33: 0.0018 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 151:260 REMARK 3 ORIGIN FOR THE GROUP (A): -6.2451 10.7297 20.1395 REMARK 3 T TENSOR REMARK 3 T11: 0.0484 T22: 0.0870 REMARK 3 T33: 0.0855 T12: 0.0136 REMARK 3 T13: 0.0046 T23: -0.0073 REMARK 3 L TENSOR REMARK 3 L11: 1.1237 L22: 0.8561 REMARK 3 L33: 2.0002 L12: -0.0594 REMARK 3 L13: -0.0154 L23: 0.1728 REMARK 3 S TENSOR REMARK 3 S11: -0.0253 S12: -0.0695 S13: 0.0600 REMARK 3 S21: 0.0229 S22: -0.0075 S23: 0.0819 REMARK 3 S31: -0.0908 S32: -0.2156 S33: -0.0160 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 261:335 REMARK 3 ORIGIN FOR THE GROUP (A): 3.0418 8.5227 -1.8842 REMARK 3 T TENSOR REMARK 3 T11: 0.1707 T22: 0.1217 REMARK 3 T33: 0.0886 T12: 0.0046 REMARK 3 T13: 0.0090 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.9437 L22: 0.9722 REMARK 3 L33: 1.1110 L12: -0.4108 REMARK 3 L13: -0.1029 L23: 0.1984 REMARK 3 S TENSOR REMARK 3 S11: 0.0407 S12: 0.1726 S13: 0.0598 REMARK 3 S21: -0.3986 S22: -0.0639 S23: -0.0922 REMARK 3 S31: -0.0355 S32: -0.0014 S33: 0.0002 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ((CHAIN T AND RESID 1:6) OR (CHAIN D AND RESID 1:5)) REMARK 3 ORIGIN FOR THE GROUP (A): 25.4511 4.1940 -2.6623 REMARK 3 T TENSOR REMARK 3 T11: 0.4011 T22: 0.5945 REMARK 3 T33: 0.3555 T12: 0.0067 REMARK 3 T13: 0.2787 T23: 0.1622 REMARK 3 L TENSOR REMARK 3 L11: 0.6604 L22: 0.9800 REMARK 3 L33: 0.8347 L12: -0.2837 REMARK 3 L13: 0.3942 L23: 0.5613 REMARK 3 S TENSOR REMARK 3 S11: 0.4273 S12: 1.1381 S13: 1.0045 REMARK 3 S21: -1.2926 S22: -0.1793 S23: -0.8028 REMARK 3 S31: -0.3286 S32: 0.4765 S33: -0.3917 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): 12.7442 16.0782 14.4572 REMARK 3 T TENSOR REMARK 3 T11: 0.1487 T22: 0.1184 REMARK 3 T33: 0.1537 T12: -0.0378 REMARK 3 T13: 0.0196 T23: -0.0098 REMARK 3 L TENSOR REMARK 3 L11: 0.2733 L22: 0.1719 REMARK 3 L33: 0.2218 L12: -0.1968 REMARK 3 L13: 0.0055 L23: 0.0210 REMARK 3 S TENSOR REMARK 3 S11: -0.0174 S12: -0.0802 S13: 0.1422 REMARK 3 S21: -0.0794 S22: -0.0488 S23: -0.3116 REMARK 3 S31: 0.0008 S32: -0.0606 S33: -0.0045 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): 18.9195 30.5397 17.8017 REMARK 3 T TENSOR REMARK 3 T11: 0.2287 T22: 0.1153 REMARK 3 T33: 0.4997 T12: -0.1310 REMARK 3 T13: 0.0049 T23: -0.1319 REMARK 3 L TENSOR REMARK 3 L11: 1.2345 L22: 4.8042 REMARK 3 L33: 2.5791 L12: -0.5568 REMARK 3 L13: 0.3316 L23: -1.9742 REMARK 3 S TENSOR REMARK 3 S11: 0.0778 S12: -0.4047 S13: 0.6012 REMARK 3 S21: -0.5325 S22: -1.1076 S23: -0.8884 REMARK 3 S31: 0.0553 S32: -0.1617 S33: -1.5042 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 9Y19 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_1000299616. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JAN-25 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 : 57170 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.370 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.12 REMARK 200 R MERGE FOR SHELL (I) : 0.29600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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 (%): 44.90 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 39.63750 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: 5910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 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 722 O HOH A 850 1.95 REMARK 500 O HOH A 732 O HOH A 859 1.95 REMARK 500 OE1 GLN A 213 O HOH A 501 1.99 REMARK 500 O HOH A 539 O HOH A 809 1.99 REMARK 500 O HOH P 117 O HOH P 123 2.04 REMARK 500 O HOH A 832 O HOH T 148 2.05 REMARK 500 O HOH A 828 O HOH A 857 2.06 REMARK 500 O HOH A 864 O HOH A 887 2.07 REMARK 500 O HOH D 103 O HOH D 118 2.09 REMARK 500 O HOH T 108 O HOH P 110 2.12 REMARK 500 O HOH A 725 O HOH A 812 2.15 REMARK 500 O HOH A 508 O HOH A 640 2.15 REMARK 500 O HOH A 702 O HOH A 882 2.16 REMARK 500 O HOH A 689 O HOH A 736 2.16 REMARK 500 O HOH A 721 O HOH A 889 2.17 REMARK 500 OP2 DG P 7 O HOH P 101 2.17 REMARK 500 O HOH A 726 O HOH A 874 2.17 REMARK 500 O HOH A 690 O HOH A 810 2.17 REMARK 500 O HOH A 744 O HOH A 836 2.18 REMARK 500 O HOH A 812 O HOH A 817 2.19 REMARK 500 O HOH A 694 O HOH A 866 2.19 REMARK 500 O HOH A 805 O HOH A 880 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 743 O HOH A 857 1554 2.05 REMARK 500 O HOH A 645 O HOH A 862 1556 2.12 REMARK 500 O HOH A 743 O HOH A 828 1554 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DG P 1 O3' DG P 1 C3' -0.039 REMARK 500 DG P 9 O3' DG P 9 C3' -0.042 REMARK 500 DG D 1 P DG D 1 OP3 -0.141 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 D 3 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG D 5 O4' - C1' - N9 ANGL. DEV. = 1.9 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 -151.46 -105.21 REMARK 500 ASN A 294 -168.38 -126.85 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 T 161 DISTANCE = 6.62 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 91.4 REMARK 620 3 VAL A 65 O 89.5 97.3 REMARK 620 4 HOH A 778 O 87.9 85.4 176.3 REMARK 620 5 DC D 3 OP1 170.7 97.9 89.6 92.5 REMARK 620 6 HOH D 104 O 91.5 173.5 88.5 88.9 79.1 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 98.0 REMARK 620 3 ILE A 106 O 96.8 91.0 REMARK 620 4 HOH A 747 O 82.0 95.4 173.6 REMARK 620 5 DG P 9 OP1 165.5 94.5 90.3 89.5 REMARK 620 6 HOH P 105 O 79.9 175.9 85.8 87.9 88.1 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 OD1 REMARK 620 2 ASP A 192 OD2 94.9 REMARK 620 3 DUP A 405 O2A 95.4 92.4 REMARK 620 4 DUP A 405 O1B 171.1 90.8 91.1 REMARK 620 5 DUP A 405 O1G 88.2 176.6 88.6 85.9 REMARK 620 6 HOH A 625 O 86.2 85.6 177.5 87.5 93.3 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 OD2 REMARK 620 2 ASP A 192 OD1 116.4 REMARK 620 3 ASP A 256 OD2 102.0 98.8 REMARK 620 4 DUP A 405 O2A 85.5 93.4 160.8 REMARK 620 5 HOH A 523 O 69.2 169.5 88.2 77.9 REMARK 620 6 DC P 10 O3' 155.7 85.7 62.4 104.1 90.7 REMARK 620 N 1 2 3 4 5 DBREF 9Y19 A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 9Y19 T 1 16 PDB 9Y19 9Y19 1 16 DBREF 9Y19 P 1 10 PDB 9Y19 9Y19 1 10 DBREF 9Y19 D 1 5 PDB 9Y19 9Y19 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 MG A 403 1 HET MG A 404 1 HET DUP A 405 28 HET CL A 406 1 HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM CL CHLORIDE ION FORMUL 5 NA 2(NA 1+) FORMUL 7 MG 2(MG 2+) FORMUL 9 DUP C9 H16 N3 O13 P3 FORMUL 10 CL CL 1- FORMUL 11 HOH *505(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 GLY A 290 1 16 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 2.54 LINK O LEU A 62 NA NA A 401 1555 1555 2.30 LINK O VAL A 65 NA NA A 401 1555 1555 2.25 LINK O THR A 101 NA NA A 402 1555 1555 2.22 LINK O VAL A 103 NA NA A 402 1555 1555 2.36 LINK O ILE A 106 NA NA A 402 1555 1555 2.34 LINK OD1 ASP A 190 MG MG A 403 1555 1555 2.00 LINK OD2 ASP A 190 MG MG A 404 1555 1555 2.20 LINK OD2 ASP A 192 MG MG A 403 1555 1555 2.03 LINK OD1 ASP A 192 MG MG A 404 1555 1555 2.07 LINK OD2 ASP A 256 MG MG A 404 1555 1555 2.21 LINK NA NA A 401 O HOH A 778 1555 1555 2.57 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.62 LINK NA NA A 401 O HOH D 104 1555 1555 2.70 LINK NA NA A 402 O HOH A 747 1555 1555 2.32 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.40 LINK NA NA A 402 O HOH P 105 1555 1555 2.56 LINK MG MG A 403 O2A DUP A 405 1555 1555 2.10 LINK MG MG A 403 O1B DUP A 405 1555 1555 2.04 LINK MG MG A 403 O1G DUP A 405 1555 1555 2.04 LINK MG MG A 403 O HOH A 625 1555 1555 2.14 LINK MG MG A 404 O2A DUP A 405 1555 1555 2.31 LINK MG MG A 404 O HOH A 523 1555 1555 2.26 LINK MG MG A 404 O3' DC P 10 1555 1555 2.84 CISPEP 1 GLY A 274 SER A 275 0 2.50 CRYST1 50.678 79.275 55.497 90.00 107.24 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 0.019732 0.000000 0.006123 0.00000 SCALE2 0.000000 0.012614 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018867 0.00000 CONECT 388 3268 CONECT 406 3268 CONECT 425 3268 CONECT 710 3269 CONECT 728 3269 CONECT 745 3269 CONECT 1429 3270 CONECT 1430 3271 CONECT 1445 3271 CONECT 1446 3270 CONECT 1975 3271 CONECT 3120 3269 CONECT 3149 3271 CONECT 3205 3268 CONECT 3268 388 406 425 3205 CONECT 3268 3578 3789 CONECT 3269 710 728 745 3120 CONECT 3269 3547 3758 CONECT 3270 1429 1446 3290 3293 CONECT 3270 3298 3425 CONECT 3271 1430 1445 1975 3149 CONECT 3271 3290 3323 CONECT 3272 3273 CONECT 3273 3272 3274 3276 CONECT 3274 3273 3275 CONECT 3275 3274 3279 CONECT 3276 3273 3277 CONECT 3277 3276 3278 3279 CONECT 3278 3277 CONECT 3279 3275 3277 3280 CONECT 3280 3279 3281 3284 CONECT 3281 3280 3282 CONECT 3282 3281 3283 3285 CONECT 3283 3282 CONECT 3284 3280 3285 CONECT 3285 3282 3284 3286 CONECT 3286 3285 3287 CONECT 3287 3286 3288 CONECT 3288 3287 3289 3290 3291 CONECT 3289 3288 CONECT 3290 3270 3271 3288 CONECT 3291 3288 3292 CONECT 3292 3291 3293 3294 3295 CONECT 3293 3270 3292 CONECT 3294 3292 CONECT 3295 3292 3296 CONECT 3296 3295 3297 3298 3299 CONECT 3297 3296 CONECT 3298 3270 3296 CONECT 3299 3296 CONECT 3323 3271 CONECT 3425 3270 CONECT 3547 3269 CONECT 3578 3268 CONECT 3758 3269 CONECT 3789 3268 MASTER 515 0 6 19 9 0 0 6 3783 4 56 30 END