HEADER REPLICATION, HYDROLASE/DNA 29-AUG-25 9Y1A TITLE WT HUMAN DNA POLYMERASE BETA, TERNARY COMPLEX DT:DAMPCPP 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 9Y1A 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. 1.93 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 60098 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 5950 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 24.9700 - 5.9700 0.98 1836 200 0.1362 0.1435 REMARK 3 2 5.9700 - 4.7500 1.00 1846 206 0.1406 0.1922 REMARK 3 3 4.7500 - 4.1500 1.00 1841 204 0.1142 0.1541 REMARK 3 4 4.1500 - 3.7700 1.00 1876 186 0.1185 0.1487 REMARK 3 5 3.7700 - 3.5000 1.00 1892 185 0.1241 0.1672 REMARK 3 6 3.5000 - 3.3000 1.00 1836 191 0.1340 0.1925 REMARK 3 7 3.3000 - 3.1300 0.99 1852 199 0.1498 0.1802 REMARK 3 8 3.1300 - 3.0000 0.99 1830 221 0.1549 0.2026 REMARK 3 9 3.0000 - 2.8800 1.00 1877 189 0.1584 0.1989 REMARK 3 10 2.8800 - 2.7800 1.00 1814 234 0.1563 0.2119 REMARK 3 11 2.7800 - 2.7000 1.00 1863 190 0.1618 0.2095 REMARK 3 12 2.7000 - 2.6200 1.00 1837 183 0.1615 0.2229 REMARK 3 13 2.6200 - 2.5500 1.00 1813 224 0.1576 0.2105 REMARK 3 14 2.5500 - 2.4900 0.99 1898 190 0.1568 0.2091 REMARK 3 15 2.4900 - 2.4300 1.00 1818 204 0.1638 0.2128 REMARK 3 16 2.4300 - 2.3800 0.99 1850 223 0.1596 0.2350 REMARK 3 17 2.3800 - 2.3300 0.99 1803 194 0.1702 0.1982 REMARK 3 18 2.3300 - 2.2900 0.99 1855 225 0.1788 0.2274 REMARK 3 19 2.2900 - 2.2500 0.98 1812 177 0.1716 0.2277 REMARK 3 20 2.2500 - 2.2100 0.98 1816 229 0.1743 0.2380 REMARK 3 21 2.2100 - 2.1700 0.98 1827 215 0.1701 0.2360 REMARK 3 22 2.1700 - 2.1400 0.99 1771 198 0.1740 0.2202 REMARK 3 23 2.1400 - 2.1100 0.96 1807 205 0.1753 0.2208 REMARK 3 24 2.1100 - 2.0800 0.98 1797 209 0.1870 0.2438 REMARK 3 25 2.0800 - 2.0500 0.97 1782 216 0.1925 0.2556 REMARK 3 26 2.0500 - 2.0200 0.93 1742 160 0.2014 0.2293 REMARK 3 27 2.0200 - 2.0000 0.91 1714 194 0.2163 0.2749 REMARK 3 28 2.0000 - 1.9700 0.89 1660 147 0.2336 0.2924 REMARK 3 29 1.9700 - 1.9500 0.87 1617 162 0.2312 0.2734 REMARK 3 30 1.9500 - 1.9300 0.85 1566 190 0.2687 0.2950 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.80 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 3440 REMARK 3 ANGLE : 0.889 4777 REMARK 3 CHIRALITY : 0.049 521 REMARK 3 PLANARITY : 0.008 507 REMARK 3 DIHEDRAL : 19.702 1365 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): 22.3568 -8.3331 10.1937 REMARK 3 T TENSOR REMARK 3 T11: 0.0985 T22: 0.1405 REMARK 3 T33: 0.0984 T12: 0.0295 REMARK 3 T13: -0.0060 T23: -0.0275 REMARK 3 L TENSOR REMARK 3 L11: 1.0059 L22: 1.4070 REMARK 3 L33: 1.0333 L12: 0.0158 REMARK 3 L13: 0.5125 L23: -0.0747 REMARK 3 S TENSOR REMARK 3 S11: 0.0428 S12: 0.0298 S13: -0.0080 REMARK 3 S21: -0.0151 S22: -0.0112 S23: -0.1251 REMARK 3 S31: 0.2081 S32: 0.2308 S33: -0.0006 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 91:150 REMARK 3 ORIGIN FOR THE GROUP (A): 17.1609 7.1667 30.6472 REMARK 3 T TENSOR REMARK 3 T11: 0.1162 T22: 0.1691 REMARK 3 T33: 0.1346 T12: 0.0104 REMARK 3 T13: -0.0211 T23: -0.0111 REMARK 3 L TENSOR REMARK 3 L11: 0.8440 L22: 0.6286 REMARK 3 L33: 0.6769 L12: 0.1274 REMARK 3 L13: -0.1626 L23: -0.0409 REMARK 3 S TENSOR REMARK 3 S11: 0.0579 S12: -0.3109 S13: -0.0879 REMARK 3 S21: 0.1249 S22: -0.0375 S23: -0.1419 REMARK 3 S31: 0.0161 S32: 0.1773 S33: -0.0022 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 151:260 REMARK 3 ORIGIN FOR THE GROUP (A): -6.3809 10.8709 20.2658 REMARK 3 T TENSOR REMARK 3 T11: 0.0445 T22: 0.0995 REMARK 3 T33: 0.0948 T12: 0.0091 REMARK 3 T13: 0.0075 T23: -0.0073 REMARK 3 L TENSOR REMARK 3 L11: 0.9878 L22: 0.8791 REMARK 3 L33: 1.7986 L12: 0.0729 REMARK 3 L13: 0.1428 L23: 0.3285 REMARK 3 S TENSOR REMARK 3 S11: -0.0203 S12: -0.0880 S13: 0.0849 REMARK 3 S21: 0.0495 S22: 0.0047 S23: 0.0861 REMARK 3 S31: -0.0552 S32: -0.2025 S33: -0.0205 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 261:335 REMARK 3 ORIGIN FOR THE GROUP (A): 2.9660 8.4133 -1.6484 REMARK 3 T TENSOR REMARK 3 T11: 0.1529 T22: 0.1174 REMARK 3 T33: 0.0932 T12: 0.0053 REMARK 3 T13: 0.0122 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.0133 L22: 1.0955 REMARK 3 L33: 1.2107 L12: -0.3390 REMARK 3 L13: 0.0321 L23: 0.3217 REMARK 3 S TENSOR REMARK 3 S11: 0.0693 S12: 0.1652 S13: 0.0167 REMARK 3 S21: -0.3951 S22: -0.0452 S23: -0.0745 REMARK 3 S31: -0.0114 S32: 0.0723 S33: 0.0071 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): 25.5636 4.3780 -2.6906 REMARK 3 T TENSOR REMARK 3 T11: 0.3068 T22: 0.4248 REMARK 3 T33: 0.3350 T12: -0.0303 REMARK 3 T13: 0.1993 T23: 0.1315 REMARK 3 L TENSOR REMARK 3 L11: 0.6189 L22: 0.7824 REMARK 3 L33: 0.9109 L12: -0.6336 REMARK 3 L13: -0.1111 L23: 0.5044 REMARK 3 S TENSOR REMARK 3 S11: 0.3477 S12: 0.5940 S13: 0.9407 REMARK 3 S21: -0.9291 S22: -0.1536 S23: -0.8182 REMARK 3 S31: -0.4260 S32: 0.3702 S33: -0.0951 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): 12.5656 15.9655 14.6355 REMARK 3 T TENSOR REMARK 3 T11: 0.1470 T22: 0.1217 REMARK 3 T33: 0.1387 T12: -0.0385 REMARK 3 T13: 0.0228 T23: -0.0107 REMARK 3 L TENSOR REMARK 3 L11: 0.0689 L22: 0.2593 REMARK 3 L33: 0.2731 L12: -0.1862 REMARK 3 L13: -0.0768 L23: 0.1059 REMARK 3 S TENSOR REMARK 3 S11: 0.0060 S12: -0.0704 S13: 0.0461 REMARK 3 S21: -0.0225 S22: -0.0397 S23: -0.1890 REMARK 3 S31: 0.0208 S32: 0.0348 S33: -0.0002 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 30.4041 17.8028 REMARK 3 T TENSOR REMARK 3 T11: 0.2319 T22: 0.0918 REMARK 3 T33: 0.5344 T12: -0.1327 REMARK 3 T13: 0.0217 T23: -0.0988 REMARK 3 L TENSOR REMARK 3 L11: 0.8754 L22: 3.0170 REMARK 3 L33: 2.0625 L12: 0.0707 REMARK 3 L13: 0.3485 L23: -1.7388 REMARK 3 S TENSOR REMARK 3 S11: -0.0671 S12: -0.4965 S13: 0.4673 REMARK 3 S21: -0.3150 S22: -0.8696 S23: -0.9525 REMARK 3 S31: 0.1597 S32: 0.0046 S33: -1.4820 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 9Y1A 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_1000299620. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-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 : 60098 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 24.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.730 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.46900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 (%): 44.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 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 39.51600 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: 5230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 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 630 O HOH A 807 2.03 REMARK 500 O HOH A 763 O HOH A 844 2.07 REMARK 500 O HOH A 622 O HOH A 785 2.07 REMARK 500 O HOH A 694 O HOH A 832 2.07 REMARK 500 OE1 GLN A 213 O HOH A 501 2.12 REMARK 500 OP2 DG P 7 O HOH P 101 2.12 REMARK 500 O HOH T 144 O HOH P 131 2.14 REMARK 500 O HOH T 119 O HOH P 111 2.14 REMARK 500 O HOH A 780 O HOH A 812 2.14 REMARK 500 O HOH A 703 O HOH A 830 2.14 REMARK 500 OE1 GLU A 216 O HOH A 502 2.16 REMARK 500 O HOH A 750 O HOH A 830 2.16 REMARK 500 OG1 THR A 304 O HOH A 503 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 846 O HOH A 849 2555 2.14 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 -0.118 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 -154.68 -109.53 REMARK 500 ASN A 294 -167.22 -129.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 885 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH T 164 DISTANCE = 6.09 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 94.3 REMARK 620 3 VAL A 65 O 91.6 97.8 REMARK 620 4 HOH A 741 O 90.6 78.2 175.5 REMARK 620 5 DC D 3 OP1 170.2 95.5 87.3 91.2 REMARK 620 6 HOH D 101 O 93.4 169.8 88.7 95.0 76.9 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 96.5 REMARK 620 3 ILE A 106 O 97.1 89.8 REMARK 620 4 HOH A 797 O 82.0 91.0 178.8 REMARK 620 5 DG P 9 OP1 165.3 92.8 94.4 86.4 REMARK 620 6 HOH P 105 O 78.5 174.9 91.1 88.1 92.2 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 95.2 REMARK 620 3 F2A A 405 O2B 170.6 89.0 REMARK 620 4 F2A A 405 O1A 97.7 92.2 90.5 REMARK 620 5 F2A A 405 O3G 88.0 170.5 86.6 96.2 REMARK 620 6 HOH A 571 O 80.6 81.9 91.7 173.7 89.8 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 113.9 REMARK 620 3 ASP A 256 OD2 104.5 97.3 REMARK 620 4 F2A A 405 O1A 86.7 90.2 162.4 REMARK 620 5 HOH A 536 O 72.6 164.2 94.7 75.5 REMARK 620 6 DC P 10 O3' 160.2 85.9 70.8 94.0 88.4 REMARK 620 N 1 2 3 4 5 DBREF 9Y1A A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 9Y1A T 1 16 PDB 9Y1A 9Y1A 1 16 DBREF 9Y1A P 1 10 PDB 9Y1A 9Y1A 1 10 DBREF 9Y1A D 1 5 PDB 9Y1A 9Y1A 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 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 HET CL A 406 1 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 HETNAM CL CHLORIDE ION FORMUL 5 NA 2(NA 1+) FORMUL 7 MG 2(MG 2+) FORMUL 9 F2A C11 H18 N5 O11 P3 FORMUL 10 CL CL 1- FORMUL 11 HOH *502(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 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 2.48 LINK O LEU A 62 NA NA A 401 1555 1555 2.30 LINK O VAL A 65 NA NA A 401 1555 1555 2.26 LINK O THR A 101 NA NA A 402 1555 1555 2.28 LINK O VAL A 103 NA NA A 402 1555 1555 2.52 LINK O ILE A 106 NA NA A 402 1555 1555 2.30 LINK OD1 ASP A 190 MG MG A 403 1555 1555 1.98 LINK OD2 ASP A 190 MG MG A 404 1555 1555 2.05 LINK OD2 ASP A 192 MG MG A 403 1555 1555 2.07 LINK OD1 ASP A 192 MG MG A 404 1555 1555 2.05 LINK OD2 ASP A 256 MG MG A 404 1555 1555 2.13 LINK NA NA A 401 O HOH A 741 1555 1555 2.60 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.61 LINK NA NA A 401 O HOH D 101 1555 1555 2.70 LINK NA NA A 402 O HOH A 797 1555 1555 2.54 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.42 LINK NA NA A 402 O HOH P 105 1555 1555 2.54 LINK MG MG A 403 O2B F2A A 405 1555 1555 2.02 LINK MG MG A 403 O1A F2A A 405 1555 1555 2.14 LINK MG MG A 403 O3G F2A A 405 1555 1555 2.08 LINK MG MG A 403 O HOH A 571 1555 1555 2.14 LINK MG MG A 404 O1A F2A A 405 1555 1555 2.29 LINK MG MG A 404 O HOH A 536 1555 1555 2.40 LINK MG MG A 404 O3' DC P 10 1555 1555 2.38 CISPEP 1 GLY A 274 SER A 275 0 2.49 CRYST1 50.616 79.032 55.556 90.00 107.39 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 0.019757 0.000000 0.006188 0.00000 SCALE2 0.000000 0.012653 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018862 0.00000 CONECT 388 3283 CONECT 406 3283 CONECT 425 3283 CONECT 710 3284 CONECT 728 3284 CONECT 745 3284 CONECT 1440 3285 CONECT 1441 3286 CONECT 1456 3286 CONECT 1457 3285 CONECT 1998 3286 CONECT 3135 3284 CONECT 3164 3286 CONECT 3220 3283 CONECT 3283 388 406 425 3220 CONECT 3283 3558 3803 CONECT 3284 710 728 745 3135 CONECT 3284 3614 3771 CONECT 3285 1440 1457 3288 3294 CONECT 3285 3299 3388 CONECT 3286 1441 1456 1998 3164 CONECT 3286 3288 3353 CONECT 3287 3288 3289 3290 3291 CONECT 3288 3285 3286 3287 CONECT 3289 3287 CONECT 3290 3287 3292 CONECT 3291 3287 3300 CONECT 3292 3290 3293 3294 3295 CONECT 3293 3292 CONECT 3294 3285 3292 CONECT 3295 3292 3296 CONECT 3296 3295 3297 3298 3299 CONECT 3297 3296 CONECT 3298 3296 CONECT 3299 3285 3296 CONECT 3300 3291 3301 CONECT 3301 3300 3302 3315 CONECT 3302 3301 3303 CONECT 3303 3302 3304 3314 CONECT 3304 3303 3305 3313 CONECT 3305 3304 3306 3311 CONECT 3306 3305 3307 CONECT 3307 3306 3308 CONECT 3308 3307 3309 CONECT 3309 3308 3310 3311 CONECT 3310 3309 CONECT 3311 3305 3309 3312 CONECT 3312 3311 3313 CONECT 3313 3304 3312 CONECT 3314 3303 3315 CONECT 3315 3301 3314 3316 CONECT 3316 3315 CONECT 3353 3286 CONECT 3388 3285 CONECT 3558 3283 CONECT 3614 3284 CONECT 3771 3284 CONECT 3803 3283 MASTER 490 0 6 19 9 0 0 6 3779 4 58 30 END