HEADER TRANSFERASE/DNA 14-AUG-13 4M9G TITLE DNA POLYMERASE BETA E295K BINARY COMPLEX 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 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA TEMPLATE STRAND; COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA PRIMER STRAND; COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA DOWNSTREAM STRAND; COMPND 17 CHAIN: D; COMPND 18 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 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: DNA TEMPLATE STRAND, 16MER; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: DNA PRIMER STRAND, 10MER; SOURCE 17 MOL_ID: 4; SOURCE 18 SYNTHETIC: YES; SOURCE 19 OTHER_DETAILS: DNA DOWNSTREAM STRAND, 5MER KEYWDS DNA POLYMERASE, LYASE, DNA COMPLEX, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.E.ECKENROTH,S.DOUBLIE REVDAT 5 28-FEB-24 4M9G 1 REMARK SEQADV LINK REVDAT 4 15-NOV-17 4M9G 1 REMARK REVDAT 3 18-DEC-13 4M9G 1 JRNL REVDAT 2 30-OCT-13 4M9G 1 JRNL REVDAT 1 16-OCT-13 4M9G 0 JRNL AUTH B.E.ECKENROTH,J.B.TOWLE-WEICKSEL,J.B.SWEASY,S.DOUBLIE JRNL TITL THE E295K CANCER VARIANT OF HUMAN POLYMERASE BETA FAVORS THE JRNL TITL 2 MISMATCH CONFORMATIONAL PATHWAY DURING NUCLEOTIDE SELECTION. JRNL REF J.BIOL.CHEM. V. 288 34850 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 24133209 JRNL DOI 10.1074/JBC.M113.510891 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 56743 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.060 REMARK 3 FREE R VALUE TEST SET COUNT : 5711 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 13.7009 - 6.0653 1.00 1711 233 0.1581 0.1716 REMARK 3 2 6.0653 - 4.8857 1.00 1789 181 0.1642 0.2068 REMARK 3 3 4.8857 - 4.2898 1.00 1798 179 0.1418 0.1657 REMARK 3 4 4.2898 - 3.9076 0.99 1723 184 0.1485 0.1851 REMARK 3 5 3.9076 - 3.6331 0.99 1708 229 0.1530 0.1845 REMARK 3 6 3.6331 - 3.4224 0.99 1777 177 0.1663 0.2129 REMARK 3 7 3.4224 - 3.2534 0.99 1765 176 0.1679 0.2258 REMARK 3 8 3.2534 - 3.1135 0.99 1701 217 0.1868 0.2253 REMARK 3 9 3.1135 - 2.9949 0.98 1735 185 0.2014 0.2405 REMARK 3 10 2.9949 - 2.8926 0.98 1765 170 0.1997 0.2579 REMARK 3 11 2.8926 - 2.8029 0.98 1782 146 0.1924 0.2521 REMARK 3 12 2.8029 - 2.7235 0.98 1690 224 0.1941 0.2277 REMARK 3 13 2.7235 - 2.6523 0.98 1717 211 0.1963 0.2568 REMARK 3 14 2.6523 - 2.5880 0.97 1712 195 0.1985 0.2408 REMARK 3 15 2.5880 - 2.5296 0.98 1725 194 0.1967 0.2506 REMARK 3 16 2.5296 - 2.4760 0.97 1680 183 0.1923 0.2470 REMARK 3 17 2.4760 - 2.4268 0.97 1788 184 0.2009 0.2344 REMARK 3 18 2.4268 - 2.3812 0.97 1695 164 0.1980 0.2521 REMARK 3 19 2.3812 - 2.3389 0.97 1726 194 0.1961 0.2653 REMARK 3 20 2.3389 - 2.2995 0.96 1676 179 0.2173 0.2353 REMARK 3 21 2.2995 - 2.2625 0.97 1705 205 0.2174 0.2629 REMARK 3 22 2.2625 - 2.2279 0.96 1722 195 0.2158 0.2534 REMARK 3 23 2.2279 - 2.1952 0.96 1654 181 0.2341 0.2552 REMARK 3 24 2.1952 - 2.1644 0.96 1688 203 0.2398 0.2749 REMARK 3 25 2.1644 - 2.1353 0.95 1685 200 0.2479 0.3055 REMARK 3 26 2.1353 - 2.1077 0.95 1637 195 0.2602 0.2961 REMARK 3 27 2.1077 - 2.0814 0.94 1639 220 0.2598 0.2850 REMARK 3 28 2.0814 - 2.0564 0.92 1665 181 0.2801 0.3097 REMARK 3 29 2.0564 - 2.0326 0.89 1523 170 0.2911 0.2714 REMARK 3 30 2.0326 - 2.0098 0.83 1451 156 0.3140 0.3687 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.42 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 : 0.003 3222 REMARK 3 ANGLE : 0.763 4480 REMARK 3 CHIRALITY : 0.045 498 REMARK 3 PLANARITY : 0.003 472 REMARK 3 DIHEDRAL : 18.129 1246 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 11 THROUGH 102 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.6796 -2.7492 11.8460 REMARK 3 T TENSOR REMARK 3 T11: 0.1471 T22: 0.1209 REMARK 3 T33: 0.1787 T12: -0.0177 REMARK 3 T13: -0.0130 T23: 0.0368 REMARK 3 L TENSOR REMARK 3 L11: 1.7846 L22: 4.5406 REMARK 3 L33: 3.5780 L12: -0.5284 REMARK 3 L13: -0.8912 L23: 2.0882 REMARK 3 S TENSOR REMARK 3 S11: 0.0517 S12: -0.0793 S13: -0.2590 REMARK 3 S21: -0.1630 S22: -0.0372 S23: -0.2043 REMARK 3 S31: 0.2269 S32: -0.1479 S33: -0.0470 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 103 THROUGH 261 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.4679 9.1516 22.2313 REMARK 3 T TENSOR REMARK 3 T11: 0.1384 T22: 0.1083 REMARK 3 T33: 0.1313 T12: 0.0070 REMARK 3 T13: 0.0155 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 5.3390 L22: 1.1496 REMARK 3 L33: 1.2997 L12: 0.3915 REMARK 3 L13: 0.3222 L23: 0.0918 REMARK 3 S TENSOR REMARK 3 S11: 0.1059 S12: -0.1814 S13: -0.2223 REMARK 3 S21: -0.0158 S22: -0.0617 S23: 0.0762 REMARK 3 S31: 0.0130 S32: -0.1405 S33: -0.0394 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 262 THROUGH 335 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.7630 7.2509 -4.4169 REMARK 3 T TENSOR REMARK 3 T11: 0.5417 T22: 0.9147 REMARK 3 T33: 0.3160 T12: -0.2550 REMARK 3 T13: 0.1173 T23: -0.3955 REMARK 3 L TENSOR REMARK 3 L11: 1.3775 L22: 0.9254 REMARK 3 L33: 2.3372 L12: -0.1343 REMARK 3 L13: -0.6508 L23: -0.4672 REMARK 3 S TENSOR REMARK 3 S11: -0.4255 S12: 1.0666 S13: -0.6101 REMARK 3 S21: -0.9278 S22: 0.7534 S23: -0.3436 REMARK 3 S31: 0.3660 S32: -0.1801 S33: -0.0290 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.8374 13.9332 -3.0589 REMARK 3 T TENSOR REMARK 3 T11: 0.3896 T22: 0.2586 REMARK 3 T33: 0.2057 T12: 0.0738 REMARK 3 T13: 0.0445 T23: 0.0227 REMARK 3 L TENSOR REMARK 3 L11: 8.1850 L22: 2.1139 REMARK 3 L33: 5.5902 L12: 0.0064 REMARK 3 L13: -2.0989 L23: 2.3398 REMARK 3 S TENSOR REMARK 3 S11: 0.1117 S12: 0.3860 S13: 0.6371 REMARK 3 S21: -0.2578 S22: 0.4215 S23: -0.1255 REMARK 3 S31: -0.2329 S32: 0.4037 S33: -0.5458 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 6 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.6770 24.5469 15.0692 REMARK 3 T TENSOR REMARK 3 T11: 0.1749 T22: 0.1243 REMARK 3 T33: 0.2891 T12: 0.0033 REMARK 3 T13: 0.0000 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 2.1283 L22: 7.0179 REMARK 3 L33: 2.6627 L12: 2.0482 REMARK 3 L13: 0.7749 L23: 0.3346 REMARK 3 S TENSOR REMARK 3 S11: 0.0248 S12: 0.2803 S13: 0.0605 REMARK 3 S21: -0.0698 S22: 0.0088 S23: -0.6964 REMARK 3 S31: -0.0348 S32: 0.1795 S33: -0.1145 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.2377 25.7422 16.0072 REMARK 3 T TENSOR REMARK 3 T11: 0.1249 T22: 0.1634 REMARK 3 T33: 0.1390 T12: -0.0316 REMARK 3 T13: -0.0354 T23: -0.0119 REMARK 3 L TENSOR REMARK 3 L11: 3.4810 L22: 6.1624 REMARK 3 L33: 5.3888 L12: -0.7923 REMARK 3 L13: -0.9203 L23: 0.9369 REMARK 3 S TENSOR REMARK 3 S11: 0.1953 S12: -0.1045 S13: 0.4614 REMARK 3 S21: -0.5992 S22: -0.4271 S23: -0.2582 REMARK 3 S31: -0.4087 S32: -0.0772 S33: 0.1395 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.4422 6.1979 -4.1413 REMARK 3 T TENSOR REMARK 3 T11: 0.4368 T22: 0.2450 REMARK 3 T33: 0.1583 T12: 0.0125 REMARK 3 T13: 0.0048 T23: 0.0452 REMARK 3 L TENSOR REMARK 3 L11: 5.2088 L22: 2.0348 REMARK 3 L33: 5.7209 L12: 0.4758 REMARK 3 L13: -0.9284 L23: -3.1737 REMARK 3 S TENSOR REMARK 3 S11: 0.2014 S12: 0.8411 S13: 0.2244 REMARK 3 S21: -0.4376 S22: -0.0032 S23: 0.2215 REMARK 3 S31: 0.3310 S32: 0.0157 S33: -0.1042 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4M9G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081633. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 104 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 14.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.67400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ISOMORPHOUS REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG 3350, 300 MM SODIUM ACETATE PH REMARK 280 9, 50 MM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 39.70950 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: 3940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 465 THR A 10 REMARK 465 GLU A 203 REMARK 465 SER A 204 REMARK 465 THR A 205 REMARK 465 LYS A 206 REMARK 465 GLN A 207 REMARK 465 PRO A 208 REMARK 465 LYS A 244 REMARK 465 ASN A 245 REMARK 465 ASP A 246 REMARK 465 GLU A 247 REMARK 465 LYS A 248 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 LYS A 48 CG CD CE NZ REMARK 470 LYS A 68 CE NZ REMARK 470 GLN A 90 CD OE1 NE2 REMARK 470 GLU A 129 CG CD OE1 OE2 REMARK 470 GLU A 186 CG CD OE1 OE2 REMARK 470 SER A 202 OG REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 LYS A 220 CD CE NZ REMARK 470 ILE A 277 CG1 CG2 CD1 REMARK 470 LYS A 280 CG CD CE NZ REMARK 470 HIS A 285 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 287 CG CD1 CD2 REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 LYS A 289 CD CE NZ REMARK 470 ARG A 299 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 303 CG1 CG2 REMARK 470 GLU A 309 CD OE1 OE2 REMARK 470 LYS A 317 CE NZ REMARK 470 GLN A 324 CG CD OE1 NE2 REMARK 470 LYS A 326 CG CD CE NZ REMARK 470 LYS A 331 CE NZ REMARK 470 GLU A 335 CG CD OE1 OE2 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 OP2 DG T 7 O HOH T 140 2.17 REMARK 500 O HOH A 617 O HOH A 645 2.19 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 P 10 O4' - C1' - N1 ANGL. DEV. = 2.4 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 -140.43 -102.27 REMARK 500 ASN A 294 -169.76 -118.11 REMARK 500 REMARK 500 REMARK: NULL 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 86.7 REMARK 620 3 VAL A 65 O 88.5 92.6 REMARK 620 4 HOH A 533 O 91.4 84.9 177.5 REMARK 620 5 DC D 3 OP1 177.9 92.0 89.8 90.2 REMARK 620 6 HOH D 105 O 99.1 173.4 90.7 91.7 82.3 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 93.1 REMARK 620 3 ILE A 106 O 93.0 88.4 REMARK 620 4 HOH A 513 O 80.3 96.3 172.0 REMARK 620 5 DG P 9 OP1 163.3 98.6 99.1 86.6 REMARK 620 6 HOH P 105 O 79.8 171.2 86.8 87.6 89.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4M9H RELATED DB: PDB REMARK 900 RELATED ID: 4M9J RELATED DB: PDB REMARK 900 RELATED ID: 4M9L RELATED DB: PDB REMARK 900 RELATED ID: 4M9N RELATED DB: PDB DBREF 4M9G A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 4M9G T 1 16 PDB 4M9G 4M9G 1 16 DBREF 4M9G P 1 10 PDB 4M9G 4M9G 1 10 DBREF 4M9G D 1 5 PDB 4M9G 4M9G 1 5 SEQADV 4M9G LYS A 295 UNP P06746 GLU 295 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 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 LYS 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 CL A 403 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 5 NA 2(NA 1+) FORMUL 7 CL CL 1- FORMUL 8 HOH *354(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 TYR A 49 1 18 HELIX 3 3 SER A 55 LYS A 61 1 7 HELIX 4 4 GLY A 66 GLY A 80 1 15 HELIX 5 5 LEU A 82 ASP A 91 1 10 HELIX 6 6 ASP A 91 THR A 101 1 11 HELIX 7 7 GLY A 107 GLU A 117 1 11 HELIX 8 8 THR A 121 LYS A 127 1 7 HELIX 9 9 ASN A 128 LEU A 132 5 5 HELIX 10 10 ASN A 133 TYR A 142 1 10 HELIX 11 11 TYR A 142 GLU A 147 1 6 HELIX 12 12 ARG A 152 ASP A 170 1 19 HELIX 13 13 CYS A 178 ARG A 183 1 6 HELIX 14 14 LEU A 210 VAL A 221 1 12 HELIX 15 15 PRO A 261 ASP A 263 5 3 HELIX 16 16 GLN A 264 GLY A 274 1 11 HELIX 17 17 SER A 275 LYS A 289 1 15 HELIX 18 18 SER A 315 ILE A 323 1 9 HELIX 19 19 GLU A 329 ARG A 333 5 5 SHEET 1 A 2 ILE A 150 PRO A 151 0 SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 B 5 ILE A 174 VAL A 177 0 SHEET 2 B 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 B 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195 SHEET 4 B 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 B 5 ILE A 224 LYS A 230 -1 N SER A 229 O MET A 236 SHEET 1 C 2 PHE A 291 ILE A 293 0 SHEET 2 C 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 2.37 LINK O LEU A 62 NA NA A 401 1555 1555 2.53 LINK O VAL A 65 NA NA A 401 1555 1555 2.40 LINK O THR A 101 NA NA A 402 1555 1555 2.33 LINK O VAL A 103 NA NA A 402 1555 1555 2.43 LINK O ILE A 106 NA NA A 402 1555 1555 2.35 LINK NA NA A 401 O HOH A 533 1555 1555 2.82 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.75 LINK NA NA A 401 O HOH D 105 1555 1555 2.41 LINK NA NA A 402 O HOH A 513 1555 1555 2.62 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.33 LINK NA NA A 402 O HOH P 105 1555 1555 2.49 CISPEP 1 GLY A 274 SER A 275 0 2.33 SITE 1 AC1 6 LYS A 60 LEU A 62 VAL A 65 HOH A 533 SITE 2 AC1 6 DC D 3 HOH D 105 SITE 1 AC2 6 THR A 101 VAL A 103 ILE A 106 HOH A 513 SITE 2 AC2 6 DG P 9 HOH P 105 SITE 1 AC3 1 THR A 297 CRYST1 54.424 79.419 54.806 90.00 105.25 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 0.018374 0.000000 0.005009 0.00000 SCALE2 0.000000 0.012591 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018912 0.00000