HEADER REPLICATION, HYDROLASE/DNA 29-AUG-25 9Y1C TITLE WT HUMAN DNA POLYMERASE BETA, TERNARY COMPLEX DG:DCMPCPP 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 9Y1C 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) : 20.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 59641 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.850 REMARK 3 FREE R VALUE TEST SET COUNT : 5874 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 20.6700 - 5.8600 0.98 1935 204 0.1282 0.1424 REMARK 3 2 5.8600 - 4.6700 0.99 1922 212 0.1321 0.1739 REMARK 3 3 4.6700 - 4.0800 0.99 1956 212 0.1115 0.1537 REMARK 3 4 4.0800 - 3.7100 1.00 1926 216 0.1202 0.1526 REMARK 3 5 3.7100 - 3.4500 0.99 1987 169 0.1246 0.1525 REMARK 3 6 3.4500 - 3.2500 0.99 1950 194 0.1321 0.1816 REMARK 3 7 3.2500 - 3.0800 0.96 1889 214 0.1502 0.1843 REMARK 3 8 3.0800 - 2.9500 0.94 1800 219 0.1530 0.1931 REMARK 3 9 2.9500 - 2.8400 0.93 1832 212 0.1592 0.1977 REMARK 3 10 2.8400 - 2.7400 0.92 1798 182 0.1606 0.1964 REMARK 3 11 2.7400 - 2.6500 0.90 1733 196 0.1682 0.2101 REMARK 3 12 2.6500 - 2.5800 0.90 1828 188 0.1587 0.2445 REMARK 3 13 2.5800 - 2.5100 0.90 1774 181 0.1625 0.2178 REMARK 3 14 2.5100 - 2.4500 0.90 1743 206 0.1656 0.1839 REMARK 3 15 2.4500 - 2.3900 0.90 1748 204 0.1672 0.2332 REMARK 3 16 2.3900 - 2.3400 0.90 1744 204 0.1721 0.2134 REMARK 3 17 2.3400 - 2.3000 0.89 1750 195 0.1728 0.2093 REMARK 3 18 2.3000 - 2.2500 0.90 1752 182 0.1713 0.2211 REMARK 3 19 2.2500 - 2.2100 0.89 1741 201 0.1668 0.2124 REMARK 3 20 2.2100 - 2.1700 0.90 1789 207 0.1792 0.2461 REMARK 3 21 2.1700 - 2.1400 0.88 1711 181 0.1772 0.2069 REMARK 3 22 2.1400 - 2.1100 0.89 1725 200 0.1766 0.2267 REMARK 3 23 2.1100 - 2.0800 0.89 1753 243 0.1938 0.2412 REMARK 3 24 2.0800 - 2.0500 0.88 1675 187 0.1902 0.2889 REMARK 3 25 2.0500 - 2.0200 0.88 1778 165 0.2068 0.2475 REMARK 3 26 2.0200 - 1.9900 0.86 1683 169 0.2047 0.2440 REMARK 3 27 1.9900 - 1.9700 0.88 1760 156 0.2079 0.2515 REMARK 3 28 1.9700 - 1.9400 0.87 1729 180 0.2215 0.2656 REMARK 3 29 1.9400 - 1.9200 0.86 1644 218 0.2368 0.3150 REMARK 3 30 1.9200 - 1.9000 0.86 1712 177 0.2382 0.2909 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) : 19.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.10 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 : 0.006 3451 REMARK 3 ANGLE : 0.848 4792 REMARK 3 CHIRALITY : 0.048 524 REMARK 3 PLANARITY : 0.008 507 REMARK 3 DIHEDRAL : 19.494 1374 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): 22.3487 -8.3178 10.3409 REMARK 3 T TENSOR REMARK 3 T11: 0.1279 T22: 0.1508 REMARK 3 T33: 0.1228 T12: 0.0318 REMARK 3 T13: -0.0011 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 1.1948 L22: 1.5657 REMARK 3 L33: 0.9068 L12: 0.4280 REMARK 3 L13: -0.0154 L23: 0.1867 REMARK 3 S TENSOR REMARK 3 S11: 0.0313 S12: 0.0357 S13: 0.0047 REMARK 3 S21: -0.0964 S22: 0.0158 S23: -0.1406 REMARK 3 S31: 0.1229 S32: 0.1828 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 91:150 REMARK 3 ORIGIN FOR THE GROUP (A): 17.2647 7.4481 30.4619 REMARK 3 T TENSOR REMARK 3 T11: 0.1205 T22: 0.1874 REMARK 3 T33: 0.1687 T12: 0.0015 REMARK 3 T13: -0.0217 T23: -0.0106 REMARK 3 L TENSOR REMARK 3 L11: 0.8792 L22: 0.8230 REMARK 3 L33: 0.9689 L12: -0.1136 REMARK 3 L13: -0.6091 L23: -0.2031 REMARK 3 S TENSOR REMARK 3 S11: 0.0459 S12: -0.2784 S13: -0.0631 REMARK 3 S21: 0.1055 S22: -0.0365 S23: -0.1934 REMARK 3 S31: -0.0410 S32: 0.2703 S33: -0.0006 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 151:260 REMARK 3 ORIGIN FOR THE GROUP (A): -6.2760 10.9312 20.1948 REMARK 3 T TENSOR REMARK 3 T11: 0.0609 T22: 0.1163 REMARK 3 T33: 0.1002 T12: 0.0081 REMARK 3 T13: 0.0088 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 1.2335 L22: 1.0181 REMARK 3 L33: 2.0678 L12: -0.1880 REMARK 3 L13: 0.1786 L23: 0.0461 REMARK 3 S TENSOR REMARK 3 S11: -0.0198 S12: -0.0718 S13: 0.0599 REMARK 3 S21: 0.0471 S22: 0.0069 S23: 0.1164 REMARK 3 S31: -0.1052 S32: -0.2409 S33: -0.0042 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 261:335 REMARK 3 ORIGIN FOR THE GROUP (A): 3.0741 8.8010 -1.8852 REMARK 3 T TENSOR REMARK 3 T11: 0.1937 T22: 0.1232 REMARK 3 T33: 0.1057 T12: -0.0112 REMARK 3 T13: 0.0063 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 1.2703 L22: 1.1208 REMARK 3 L33: 1.5059 L12: -0.3585 REMARK 3 L13: 0.0804 L23: 0.2783 REMARK 3 S TENSOR REMARK 3 S11: 0.0268 S12: 0.2046 S13: 0.0284 REMARK 3 S21: -0.4466 S22: -0.0214 S23: -0.0751 REMARK 3 S31: -0.0100 S32: 0.0105 S33: 0.0015 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): 25.2764 4.5706 -2.6470 REMARK 3 T TENSOR REMARK 3 T11: 0.4136 T22: 0.4111 REMARK 3 T33: 0.3502 T12: 0.0376 REMARK 3 T13: 0.1754 T23: 0.1164 REMARK 3 L TENSOR REMARK 3 L11: 0.2276 L22: 0.2106 REMARK 3 L33: 0.0099 L12: -0.2171 REMARK 3 L13: -0.0499 L23: 0.0494 REMARK 3 S TENSOR REMARK 3 S11: 0.4212 S12: 0.5185 S13: 0.8876 REMARK 3 S21: -0.7642 S22: -0.1992 S23: -0.6596 REMARK 3 S31: -0.0391 S32: 0.0587 S33: 0.0065 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): 12.5733 16.4162 14.4806 REMARK 3 T TENSOR REMARK 3 T11: 0.1498 T22: 0.1174 REMARK 3 T33: 0.1591 T12: -0.0431 REMARK 3 T13: 0.0188 T23: 0.0049 REMARK 3 L TENSOR REMARK 3 L11: 0.1708 L22: 0.2938 REMARK 3 L33: 0.6716 L12: -0.2222 REMARK 3 L13: 0.0864 L23: -0.0072 REMARK 3 S TENSOR REMARK 3 S11: -0.0374 S12: -0.0084 S13: 0.1058 REMARK 3 S21: -0.0328 S22: -0.0672 S23: -0.2427 REMARK 3 S31: -0.0381 S32: 0.2091 S33: 0.0005 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): 18.7996 30.8897 17.8908 REMARK 3 T TENSOR REMARK 3 T11: 0.3255 T22: 0.1911 REMARK 3 T33: 0.5269 T12: -0.0862 REMARK 3 T13: 0.0277 T23: -0.0509 REMARK 3 L TENSOR REMARK 3 L11: 0.5661 L22: 3.4479 REMARK 3 L33: 1.2050 L12: -0.8273 REMARK 3 L13: 0.4787 L23: -1.4127 REMARK 3 S TENSOR REMARK 3 S11: -0.1219 S12: -0.1609 S13: 0.5199 REMARK 3 S21: -0.3548 S22: -0.3687 S23: -0.8290 REMARK 3 S31: 0.1009 S32: 0.0091 S33: -0.6016 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 9Y1C 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_1000299624. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-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 : 59641 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.910 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.79 REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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 WITH 1 MM DNTP. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 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 39.84600 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: 5210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -84.0 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 OE1 GLN A 213 O HOH A 501 2.03 REMARK 500 O HOH A 552 O HOH A 799 2.03 REMARK 500 O HOH A 830 O HOH A 894 2.08 REMARK 500 O HOH A 559 O HOH A 884 2.11 REMARK 500 O HOH A 631 O HOH A 884 2.14 REMARK 500 O HOH A 807 O HOH A 899 2.14 REMARK 500 O HOH P 124 O HOH P 127 2.16 REMARK 500 O HOH A 816 O HOH D 110 2.18 REMARK 500 O HOH A 517 O HOH A 828 2.19 REMARK 500 O HOH A 826 O HOH P 124 2.19 REMARK 500 O HOH A 609 O HOH A 829 2.19 REMARK 500 O HOH A 674 O HOH A 930 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 545 O HOH A 904 1455 2.05 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 -0.128 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 -153.15 -108.34 REMARK 500 ASN A 294 -168.47 -127.08 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 168 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH T 169 DISTANCE = 6.84 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 93.4 REMARK 620 3 VAL A 65 O 92.0 96.1 REMARK 620 4 HOH A 816 O 95.0 80.1 172.2 REMARK 620 5 DC D 3 OP1 172.6 93.9 85.8 87.6 REMARK 620 6 HOH D 102 O 98.6 167.7 86.5 95.8 74.2 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 96.1 REMARK 620 3 ILE A 106 O 92.9 88.9 REMARK 620 4 HOH A 837 O 82.0 90.9 174.8 REMARK 620 5 DG P 9 OP1 163.8 97.1 96.7 88.5 REMARK 620 6 HOH P 104 O 79.7 175.5 92.7 87.2 86.9 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 104.9 REMARK 620 3 ASP A 256 OD2 95.9 95.8 REMARK 620 4 XC5 A 405 O1A 90.2 92.2 168.3 REMARK 620 5 HOH A 535 O 78.6 172.6 90.3 81.1 REMARK 620 6 DC P 10 O3' 163.9 90.1 76.6 94.9 87.1 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 97.9 REMARK 620 3 XC5 A 405 O1A 96.2 89.9 REMARK 620 4 XC5 A 405 O2B 172.3 87.2 89.5 REMARK 620 5 XC5 A 405 O1G 86.3 174.3 93.5 88.2 REMARK 620 6 HOH A 628 O 82.8 84.4 174.0 92.1 92.4 REMARK 620 N 1 2 3 4 5 DBREF 9Y1C A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 9Y1C T 1 16 PDB 9Y1C 9Y1C 1 16 DBREF 9Y1C P 1 10 PDB 9Y1C 9Y1C 1 10 DBREF 9Y1C D 1 5 PDB 9Y1C 9Y1C 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 MG A 403 1 HET MG A 404 1 HET XC5 A 405 28 HET CL A 406 1 HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETNAM XC5 2'-DEOXY-5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 2 XC5 PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE HETNAM CL CHLORIDE ION FORMUL 5 NA 2(NA 1+) FORMUL 7 MG 2(MG 2+) FORMUL 9 XC5 C10 H18 N3 O12 P3 FORMUL 10 CL CL 1- FORMUL 11 HOH *571(H2 O) HELIX 1 AA1 ASN A 12 VAL A 29 1 18 HELIX 2 AA2 ALA A 32 LYS A 48 1 17 HELIX 3 AA3 SER A 55 LYS A 61 1 7 HELIX 4 AA4 GLY A 66 GLY A 80 1 15 HELIX 5 AA5 LEU A 82 ASP A 91 1 10 HELIX 6 AA6 ASP A 91 THR A 101 1 11 HELIX 7 AA7 GLY A 107 GLU A 117 1 11 HELIX 8 AA8 THR A 121 ASN A 128 1 8 HELIX 9 AA9 GLU A 129 LEU A 132 5 4 HELIX 10 AB1 ASN A 133 TYR A 142 1 10 HELIX 11 AB2 TYR A 142 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 2.38 LINK O LEU A 62 NA NA A 401 1555 1555 2.33 LINK O VAL A 65 NA NA A 401 1555 1555 2.34 LINK O THR A 101 NA NA A 402 1555 1555 2.34 LINK O VAL A 103 NA NA A 402 1555 1555 2.40 LINK O ILE A 106 NA NA A 402 1555 1555 2.37 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 2.05 LINK OD2 ASP A 192 MG MG A 404 1555 1555 2.13 LINK OD2 ASP A 256 MG MG A 403 1555 1555 2.15 LINK NA NA A 401 O HOH A 816 1555 1555 2.58 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.71 LINK NA NA A 401 O HOH D 102 1555 1555 2.63 LINK NA NA A 402 O HOH A 837 1555 1555 2.58 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.43 LINK NA NA A 402 O HOH P 104 1555 1555 2.40 LINK MG MG A 403 O1A XC5 A 405 1555 1555 2.20 LINK MG MG A 403 O HOH A 535 1555 1555 2.13 LINK MG MG A 403 O3' DC P 10 1555 1555 2.24 LINK MG MG A 404 O1A XC5 A 405 1555 1555 2.14 LINK MG MG A 404 O2B XC5 A 405 1555 1555 2.02 LINK MG MG A 404 O1G XC5 A 405 1555 1555 2.09 LINK MG MG A 404 O HOH A 628 1555 1555 2.16 CISPEP 1 GLY A 274 SER A 275 0 1.27 CRYST1 50.690 79.692 55.506 90.00 107.44 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 0.019728 0.000000 0.006197 0.00000 SCALE2 0.000000 0.012548 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018884 0.00000 CONECT 400 3295 CONECT 418 3295 CONECT 437 3295 CONECT 728 3296 CONECT 746 3296 CONECT 763 3296 CONECT 1458 3298 CONECT 1459 3297 CONECT 1474 3297 CONECT 1475 3298 CONECT 2001 3297 CONECT 3147 3296 CONECT 3176 3297 CONECT 3232 3295 CONECT 3295 400 418 437 3232 CONECT 3295 3643 3887 CONECT 3296 728 746 763 3147 CONECT 3296 3664 3852 CONECT 3297 1459 1474 2001 3176 CONECT 3297 3300 3362 CONECT 3298 1458 1475 3300 3305 CONECT 3298 3308 3455 CONECT 3299 3300 3301 3302 3324 CONECT 3300 3297 3298 3299 CONECT 3301 3299 CONECT 3302 3299 3303 CONECT 3303 3302 3304 3305 3306 CONECT 3304 3303 CONECT 3305 3298 3303 CONECT 3306 3303 3307 CONECT 3307 3306 3308 3309 3310 CONECT 3308 3298 3307 CONECT 3309 3307 CONECT 3310 3307 CONECT 3311 3312 3316 3319 CONECT 3312 3311 3313 3317 CONECT 3313 3312 3314 CONECT 3314 3313 3315 3318 CONECT 3315 3314 3316 CONECT 3316 3311 3315 CONECT 3317 3312 CONECT 3318 3314 CONECT 3319 3311 3320 3323 CONECT 3320 3319 3321 CONECT 3321 3320 3322 3326 CONECT 3322 3321 3323 3325 CONECT 3323 3319 3322 CONECT 3324 3299 3325 CONECT 3325 3322 3324 CONECT 3326 3321 CONECT 3362 3297 CONECT 3455 3298 CONECT 3643 3295 CONECT 3664 3296 CONECT 3852 3296 CONECT 3887 3295 MASTER 482 0 6 19 9 0 0 6 3850 4 56 30 END