HEADER TRANSFERASE/DNA 14-AUG-13 4M9J TITLE DNA POLYMERASE BETA E295K SOAKED WITH 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 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 4M9J 1 REMARK SEQADV LINK REVDAT 4 24-JAN-18 4M9J 1 AUTHOR REVDAT 3 18-DEC-13 4M9J 1 JRNL REVDAT 2 30-OCT-13 4M9J 1 JRNL REVDAT 1 16-OCT-13 4M9J 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. 2.04 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 55412 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.060 REMARK 3 FREE R VALUE TEST SET COUNT : 5574 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 13.9843 - 6.1533 1.00 1645 225 0.1703 0.1924 REMARK 3 2 6.1533 - 4.9553 1.00 1699 167 0.1695 0.1935 REMARK 3 3 4.9553 - 4.3505 1.00 1711 165 0.1482 0.1836 REMARK 3 4 4.3505 - 3.9626 1.00 1686 201 0.1452 0.1646 REMARK 3 5 3.9626 - 3.6842 1.00 1657 202 0.1501 0.1717 REMARK 3 6 3.6842 - 3.4705 1.00 1702 188 0.1522 0.1709 REMARK 3 7 3.4705 - 3.2990 1.00 1724 157 0.1636 0.1931 REMARK 3 8 3.2990 - 3.1571 1.00 1700 206 0.1789 0.2531 REMARK 3 9 3.1571 - 3.0369 1.00 1636 196 0.1978 0.2644 REMARK 3 10 3.0369 - 2.9331 1.00 1732 171 0.2084 0.2597 REMARK 3 11 2.9331 - 2.8422 1.00 1719 162 0.2006 0.2346 REMARK 3 12 2.8422 - 2.7616 1.00 1680 190 0.2012 0.3260 REMARK 3 13 2.7616 - 2.6894 1.00 1683 218 0.2023 0.2874 REMARK 3 14 2.6894 - 2.6242 1.00 1674 176 0.1909 0.2749 REMARK 3 15 2.6242 - 2.5649 1.00 1676 200 0.1975 0.2877 REMARK 3 16 2.5649 - 2.5107 1.00 1684 190 0.2003 0.2375 REMARK 3 17 2.5107 - 2.4607 1.00 1697 161 0.1983 0.2895 REMARK 3 18 2.4607 - 2.4145 1.00 1715 195 0.2096 0.2597 REMARK 3 19 2.4145 - 2.3716 1.00 1734 152 0.2106 0.2800 REMARK 3 20 2.3716 - 2.3316 1.00 1686 209 0.2110 0.2827 REMARK 3 21 2.3316 - 2.2941 1.00 1648 160 0.2185 0.2503 REMARK 3 22 2.2941 - 2.2590 1.00 1697 201 0.2167 0.2452 REMARK 3 23 2.2590 - 2.2259 1.00 1736 201 0.2316 0.2892 REMARK 3 24 2.2259 - 2.1947 1.00 1635 167 0.2328 0.3249 REMARK 3 25 2.1947 - 2.1651 1.00 1730 210 0.2545 0.2908 REMARK 3 26 2.1651 - 2.1371 1.00 1603 200 0.2702 0.3355 REMARK 3 27 2.1371 - 2.1105 0.98 1659 194 0.2660 0.2840 REMARK 3 28 2.1105 - 2.0851 0.95 1574 219 0.2674 0.2945 REMARK 3 29 2.0851 - 2.0610 0.91 1548 164 0.2987 0.3551 REMARK 3 30 2.0610 - 2.0379 0.70 1168 127 0.4278 0.4869 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.34 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 : 0.002 3250 REMARK 3 ANGLE : 0.707 4527 REMARK 3 CHIRALITY : 0.042 505 REMARK 3 PLANARITY : 0.002 462 REMARK 3 DIHEDRAL : 18.319 1275 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): 31.5403 -2.9539 12.0146 REMARK 3 T TENSOR REMARK 3 T11: 0.1861 T22: 0.1428 REMARK 3 T33: 0.2204 T12: -0.0244 REMARK 3 T13: 0.0113 T23: 0.0409 REMARK 3 L TENSOR REMARK 3 L11: 2.2402 L22: 5.1361 REMARK 3 L33: 4.8337 L12: -0.8433 REMARK 3 L13: -1.3283 L23: 2.5957 REMARK 3 S TENSOR REMARK 3 S11: -0.0435 S12: -0.0920 S13: -0.3535 REMARK 3 S21: -0.1123 S22: -0.0399 S23: -0.1280 REMARK 3 S31: 0.4501 S32: -0.0078 S33: 0.0640 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 103 THROUGH 261 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.6868 8.8866 22.0123 REMARK 3 T TENSOR REMARK 3 T11: 0.1637 T22: 0.1339 REMARK 3 T33: 0.1319 T12: 0.0114 REMARK 3 T13: 0.0356 T23: 0.0113 REMARK 3 L TENSOR REMARK 3 L11: 7.2528 L22: 1.1166 REMARK 3 L33: 1.6235 L12: 0.8342 REMARK 3 L13: 1.1376 L23: 0.1209 REMARK 3 S TENSOR REMARK 3 S11: 0.0486 S12: -0.2200 S13: -0.1638 REMARK 3 S21: 0.0501 S22: 0.0120 S23: 0.0764 REMARK 3 S31: 0.0204 S32: -0.1267 S33: -0.0509 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 262 THROUGH 335 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.6952 7.3299 -3.2388 REMARK 3 T TENSOR REMARK 3 T11: 0.5108 T22: 0.8607 REMARK 3 T33: 0.3736 T12: -0.1872 REMARK 3 T13: 0.0260 T23: -0.2029 REMARK 3 L TENSOR REMARK 3 L11: 0.9481 L22: 5.2346 REMARK 3 L33: 6.5406 L12: 0.7155 REMARK 3 L13: -2.2296 L23: -4.1157 REMARK 3 S TENSOR REMARK 3 S11: -0.4717 S12: 0.7288 S13: -0.2864 REMARK 3 S21: -1.1764 S22: 0.8002 S23: -0.2000 REMARK 3 S31: 0.5261 S32: 0.0530 S33: -0.3122 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.2205 13.8061 -3.0579 REMARK 3 T TENSOR REMARK 3 T11: 0.4274 T22: 0.3050 REMARK 3 T33: 0.1933 T12: 0.1108 REMARK 3 T13: 0.0100 T23: 0.0146 REMARK 3 L TENSOR REMARK 3 L11: 9.3213 L22: 9.0233 REMARK 3 L33: 6.1563 L12: 0.9310 REMARK 3 L13: -2.5170 L23: -0.1019 REMARK 3 S TENSOR REMARK 3 S11: -0.2690 S12: 0.1700 S13: 0.3491 REMARK 3 S21: -0.4531 S22: 0.2891 S23: -0.3543 REMARK 3 S31: 0.2987 S32: 0.6219 S33: -0.0168 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 6 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.9293 22.7034 13.5027 REMARK 3 T TENSOR REMARK 3 T11: 0.2748 T22: 0.2170 REMARK 3 T33: 0.2926 T12: 0.0289 REMARK 3 T13: -0.0254 T23: 0.0657 REMARK 3 L TENSOR REMARK 3 L11: 2.4559 L22: 3.3640 REMARK 3 L33: 1.7412 L12: -0.9542 REMARK 3 L13: -1.9968 L23: 0.1972 REMARK 3 S TENSOR REMARK 3 S11: 0.2308 S12: 0.3288 S13: 0.1663 REMARK 3 S21: -0.1611 S22: -0.2341 S23: -0.4466 REMARK 3 S31: -0.1903 S32: 0.1476 S33: 0.0029 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.9385 25.2741 15.9754 REMARK 3 T TENSOR REMARK 3 T11: 0.2259 T22: 0.1858 REMARK 3 T33: 0.1723 T12: 0.0253 REMARK 3 T13: -0.0986 T23: -0.0248 REMARK 3 L TENSOR REMARK 3 L11: 5.1451 L22: 6.2492 REMARK 3 L33: 6.1959 L12: -1.4145 REMARK 3 L13: -1.6058 L23: -1.1934 REMARK 3 S TENSOR REMARK 3 S11: 0.1580 S12: 0.0128 S13: 0.4424 REMARK 3 S21: -0.8890 S22: -0.4095 S23: -0.3238 REMARK 3 S31: -0.5394 S32: -0.1063 S33: 0.2392 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.7011 6.0408 -4.1165 REMARK 3 T TENSOR REMARK 3 T11: 0.4477 T22: 0.2301 REMARK 3 T33: 0.1660 T12: -0.0012 REMARK 3 T13: -0.0347 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 8.2060 L22: 4.4299 REMARK 3 L33: 9.7332 L12: 0.0543 REMARK 3 L13: -2.5799 L23: -6.3030 REMARK 3 S TENSOR REMARK 3 S11: 0.2843 S12: 0.9006 S13: 0.0003 REMARK 3 S21: -1.1090 S22: -0.0700 S23: 0.3387 REMARK 3 S31: 0.5561 S32: -0.2141 S33: -0.2156 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 4M9J 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_1000081636. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-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) : 2.038 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.59300 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 (%): 48.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 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 39.56450 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: 5150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.0 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 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 LYS A 244 REMARK 465 ASN A 245 REMARK 465 ASP A 246 REMARK 465 GLU A 247 REMARK 465 LYS A 248 REMARK 465 LEU A 287 REMARK 465 GLU A 288 REMARK 465 LYS A 289 REMARK 465 GLY A 290 REMARK 465 GLY A 302 REMARK 465 ILE A 323 REMARK 465 GLN A 324 REMARK 465 TRP A 325 REMARK 465 LYS A 326 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 THR A 10 OG1 CG2 REMARK 470 LYS A 68 CD CE NZ REMARK 470 GLU A 123 CG CD OE1 OE2 REMARK 470 GLU A 129 CG CD OE1 OE2 REMARK 470 GLU A 186 CD OE1 OE2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 ILE A 277 CG1 CG2 CD1 REMARK 470 LYS A 280 CD CE NZ REMARK 470 ASN A 281 CG OD1 ND2 REMARK 470 HIS A 285 CG ND1 CD2 CE1 NE2 REMARK 470 VAL A 303 CG1 CG2 REMARK 470 THR A 304 OG1 CG2 REMARK 470 GLU A 309 CD OE1 OE2 REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 GLU A 329 CG CD OE1 OE2 REMARK 470 GLU A 335 CG CD OE1 OE2 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 T 5 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC P 10 O4' - C1' - N1 ANGL. DEV. = 2.9 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 -139.97 -102.99 REMARK 500 ARG A 333 47.56 -97.17 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 88.8 REMARK 620 3 VAL A 65 O 85.1 92.1 REMARK 620 4 HOH A 607 O 91.7 88.1 176.8 REMARK 620 5 DC D 3 OP1 177.2 92.4 92.3 90.9 REMARK 620 6 HOH D 111 O 93.2 177.9 87.4 92.5 85.5 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 93.5 REMARK 620 3 ILE A 106 O 94.7 88.5 REMARK 620 4 HOH A 716 O 79.5 93.6 174.0 REMARK 620 5 DG P 9 OP1 163.0 95.9 99.6 85.8 REMARK 620 6 HOH P 101 O 77.9 171.3 92.3 84.8 92.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 93.1 REMARK 620 3 DUP A 406 O2B 163.5 102.9 REMARK 620 4 DUP A 406 O1A 103.0 93.9 72.2 REMARK 620 5 DUP A 406 O3G 96.8 170.1 67.2 83.1 REMARK 620 6 HOH A 522 O 91.1 85.8 94.1 165.9 94.8 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 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUP A 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4M9G RELATED DB: PDB REMARK 900 RELATED ID: 4M9H RELATED DB: PDB REMARK 900 RELATED ID: 4M9L RELATED DB: PDB REMARK 900 RELATED ID: 4M9N RELATED DB: PDB DBREF 4M9J A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 4M9J T 1 16 PDB 4M9J 4M9J 1 16 DBREF 4M9J P 1 10 PDB 4M9J 4M9J 1 10 DBREF 4M9J D 1 5 PDB 4M9J 4M9J 1 5 SEQADV 4M9J 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 HET CL A 404 1 HET MG A 405 1 HET DUP A 406 28 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE FORMUL 5 NA 2(NA 1+) FORMUL 7 CL 2(CL 1-) FORMUL 9 MG MG 2+ FORMUL 10 DUP C9 H16 N3 O13 P3 FORMUL 11 HOH *339(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 LYS A 48 1 17 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 LYS A 209 VAL A 221 1 13 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 HIS A 285 1 11 HELIX 18 18 SER A 315 ASP A 321 1 7 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 THR A 292 ILE A 293 0 SHEET 2 C 2 ILE A 298 ARG A 299 -1 O ARG A 299 N THR A 292 LINK O LYS A 60 NA NA A 401 1555 1555 2.41 LINK O LEU A 62 NA NA A 401 1555 1555 2.58 LINK O VAL A 65 NA NA A 401 1555 1555 2.43 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 2.38 LINK OD1 ASP A 190 MG MG A 405 1555 1555 2.07 LINK OD2 ASP A 192 MG MG A 405 1555 1555 2.16 LINK NA NA A 401 O HOH A 607 1555 1555 2.59 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.66 LINK NA NA A 401 O HOH D 111 1555 1555 2.43 LINK NA NA A 402 O HOH A 716 1555 1555 2.66 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.35 LINK NA NA A 402 O HOH P 101 1555 1555 2.55 LINK MG MG A 405 O2B DUP A 406 1555 1555 1.97 LINK MG MG A 405 O1A DUP A 406 1555 1555 2.00 LINK MG MG A 405 O3G DUP A 406 1555 1555 2.16 LINK MG MG A 405 O HOH A 522 1555 1555 2.16 CISPEP 1 GLY A 274 SER A 275 0 0.97 SITE 1 AC1 6 LYS A 60 LEU A 62 VAL A 65 HOH A 607 SITE 2 AC1 6 DC D 3 HOH D 111 SITE 1 AC2 6 THR A 101 VAL A 103 ILE A 106 HOH A 716 SITE 2 AC2 6 DG P 9 HOH P 101 SITE 1 AC3 5 ALA A 32 ILE A 33 HIS A 34 HOH A 639 SITE 2 AC3 5 HOH D 110 SITE 1 AC4 1 THR A 297 SITE 1 AC5 4 ASP A 190 ASP A 192 DUP A 406 HOH A 522 SITE 1 AC6 17 GLY A 179 SER A 180 ARG A 183 SER A 188 SITE 2 AC6 17 GLY A 189 ASP A 190 ASP A 192 TYR A 271 SITE 3 AC6 17 PHE A 272 GLY A 274 MG A 405 HOH A 522 SITE 4 AC6 17 HOH A 561 HOH A 606 HOH A 651 DC P 10 SITE 5 AC6 17 DA T 6 CRYST1 54.580 79.129 54.979 90.00 105.95 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 0.018322 0.000000 0.005237 0.00000 SCALE2 0.000000 0.012638 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018917 0.00000