PDB Short entry for 4M9N HEADER TRANSFERASE/DNA 14-AUG-13 4M9N TITLE DNA POLYMERASE BETA E295K SOAKED WITH DATP 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 4 28-FEB-24 4M9N 1 REMARK SEQADV LINK REVDAT 3 18-DEC-13 4M9N 1 JRNL REVDAT 2 30-OCT-13 4M9N 1 JRNL REVDAT 1 16-OCT-13 4M9N 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. 2.28 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) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 36691 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 3646 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 13.9230 - 6.5113 0.98 1343 184 0.1792 0.1817 REMARK 3 2 6.5113 - 5.2592 0.98 1396 148 0.1849 0.1850 REMARK 3 3 5.2592 - 4.6222 0.98 1341 145 0.1541 0.1711 REMARK 3 4 4.6222 - 4.2124 0.98 1348 132 0.1486 0.1757 REMARK 3 5 4.2124 - 3.9177 0.98 1370 151 0.1590 0.1576 REMARK 3 6 3.9177 - 3.6913 0.97 1345 167 0.1726 0.2128 REMARK 3 7 3.6913 - 3.5095 0.97 1366 157 0.1701 0.2278 REMARK 3 8 3.5095 - 3.3590 0.97 1369 109 0.1887 0.2007 REMARK 3 9 3.3590 - 3.2313 0.97 1339 165 0.1937 0.2626 REMARK 3 10 3.2313 - 3.1211 0.96 1320 167 0.1986 0.2614 REMARK 3 11 3.1211 - 3.0246 0.96 1319 137 0.2116 0.2639 REMARK 3 12 3.0246 - 2.9389 0.97 1358 146 0.2209 0.2630 REMARK 3 13 2.9389 - 2.8623 0.95 1369 121 0.2138 0.2609 REMARK 3 14 2.8623 - 2.7930 0.96 1381 130 0.2197 0.2266 REMARK 3 15 2.7930 - 2.7300 0.96 1264 175 0.2145 0.3046 REMARK 3 16 2.7300 - 2.6723 0.95 1346 160 0.2313 0.2696 REMARK 3 17 2.6723 - 2.6192 0.95 1296 149 0.2235 0.2922 REMARK 3 18 2.6192 - 2.5701 0.94 1307 150 0.2218 0.3038 REMARK 3 19 2.5701 - 2.5245 0.94 1310 143 0.2408 0.2959 REMARK 3 20 2.5245 - 2.4819 0.92 1291 140 0.2340 0.3313 REMARK 3 21 2.4819 - 2.4421 0.90 1283 131 0.2348 0.2857 REMARK 3 22 2.4421 - 2.4047 0.85 1166 130 0.2287 0.2904 REMARK 3 23 2.4047 - 2.3695 0.79 1122 82 0.2436 0.2921 REMARK 3 24 2.3695 - 2.3363 0.74 1017 126 0.2442 0.3329 REMARK 3 25 2.3363 - 2.3049 0.67 939 109 0.2485 0.2956 REMARK 3 26 2.3049 - 2.2751 0.54 740 92 0.2500 0.3147 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) : 26.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.64 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 3101 REMARK 3 ANGLE : 0.598 4320 REMARK 3 CHIRALITY : 0.036 483 REMARK 3 PLANARITY : 0.002 444 REMARK 3 DIHEDRAL : 17.468 1213 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 10:79) REMARK 3 ORIGIN FOR THE GROUP (A): 30.5791 -4.3464 7.8729 REMARK 3 T TENSOR REMARK 3 T11: 0.2445 T22: 0.1478 REMARK 3 T33: 0.2145 T12: -0.0317 REMARK 3 T13: 0.0274 T23: 0.0221 REMARK 3 L TENSOR REMARK 3 L11: 2.2575 L22: 3.9670 REMARK 3 L33: 3.4165 L12: 0.0417 REMARK 3 L13: 0.2672 L23: 1.7948 REMARK 3 S TENSOR REMARK 3 S11: 0.0201 S12: 0.0093 S13: -0.4021 REMARK 3 S21: -0.3723 S22: -0.0072 S23: -0.1626 REMARK 3 S31: 0.2836 S32: -0.1938 S33: 0.0017 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 80:102) REMARK 3 ORIGIN FOR THE GROUP (A): 33.6245 1.3972 23.2442 REMARK 3 T TENSOR REMARK 3 T11: 0.1814 T22: 0.2962 REMARK 3 T33: 0.2560 T12: -0.0352 REMARK 3 T13: -0.0105 T23: 0.0482 REMARK 3 L TENSOR REMARK 3 L11: 4.0193 L22: 2.4283 REMARK 3 L33: 1.7374 L12: -2.3676 REMARK 3 L13: -1.6799 L23: 1.0267 REMARK 3 S TENSOR REMARK 3 S11: -0.0465 S12: -0.5955 S13: -0.0675 REMARK 3 S21: -0.0654 S22: 0.0785 S23: -0.3421 REMARK 3 S31: 0.0269 S32: 0.4076 S33: -0.0476 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 103:261) REMARK 3 ORIGIN FOR THE GROUP (A): 4.7085 9.2285 21.8968 REMARK 3 T TENSOR REMARK 3 T11: 0.1283 T22: 0.1438 REMARK 3 T33: 0.1364 T12: 0.0169 REMARK 3 T13: 0.0302 T23: -0.0154 REMARK 3 L TENSOR REMARK 3 L11: 5.2701 L22: 1.6582 REMARK 3 L33: 1.6364 L12: 0.2258 REMARK 3 L13: 0.9222 L23: -0.2460 REMARK 3 S TENSOR REMARK 3 S11: 0.0881 S12: -0.0993 S13: -0.1118 REMARK 3 S21: -0.0480 S22: -0.0189 S23: 0.1242 REMARK 3 S31: 0.0457 S32: -0.1578 S33: -0.0589 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 1:5) REMARK 3 ORIGIN FOR THE GROUP (A): 32.0528 13.9581 -2.9452 REMARK 3 T TENSOR REMARK 3 T11: 0.5340 T22: 0.3400 REMARK 3 T33: 0.2087 T12: 0.1404 REMARK 3 T13: 0.0716 T23: 0.0406 REMARK 3 L TENSOR REMARK 3 L11: 3.9013 L22: 4.0724 REMARK 3 L33: 3.4523 L12: -0.7245 REMARK 3 L13: -1.2402 L23: -0.0472 REMARK 3 S TENSOR REMARK 3 S11: 0.0095 S12: 0.0489 S13: 0.2882 REMARK 3 S21: -0.2359 S22: 0.0630 S23: -0.2911 REMARK 3 S31: 0.0224 S32: 0.3450 S33: -0.0483 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 6:16) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4177 24.3285 14.9497 REMARK 3 T TENSOR REMARK 3 T11: 0.2621 T22: 0.1697 REMARK 3 T33: 0.3237 T12: 0.0155 REMARK 3 T13: 0.0300 T23: 0.0271 REMARK 3 L TENSOR REMARK 3 L11: 2.1495 L22: 5.9339 REMARK 3 L33: 1.4045 L12: 0.6972 REMARK 3 L13: 0.3829 L23: 0.0297 REMARK 3 S TENSOR REMARK 3 S11: 0.0333 S12: 0.2466 S13: 0.2159 REMARK 3 S21: -0.2270 S22: 0.0769 S23: -0.5095 REMARK 3 S31: -0.1082 S32: 0.1420 S33: -0.0810 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1:10) REMARK 3 ORIGIN FOR THE GROUP (A): 16.9132 25.5671 15.8491 REMARK 3 T TENSOR REMARK 3 T11: 0.2107 T22: 0.1853 REMARK 3 T33: 0.2894 T12: -0.0431 REMARK 3 T13: -0.0584 T23: -0.0368 REMARK 3 L TENSOR REMARK 3 L11: 2.3868 L22: 7.3204 REMARK 3 L33: 3.7149 L12: -1.1577 REMARK 3 L13: -0.8814 L23: 0.5591 REMARK 3 S TENSOR REMARK 3 S11: 0.1027 S12: -0.1107 S13: 0.4033 REMARK 3 S21: -0.7948 S22: -0.3511 S23: 0.0165 REMARK 3 S31: -0.2272 S32: -0.1631 S33: 0.2705 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1:5) REMARK 3 ORIGIN FOR THE GROUP (A): 31.5865 6.2669 -4.1075 REMARK 3 T TENSOR REMARK 3 T11: 0.3967 T22: 0.2394 REMARK 3 T33: 0.2192 T12: -0.0753 REMARK 3 T13: -0.0340 T23: 0.0914 REMARK 3 L TENSOR REMARK 3 L11: 3.9595 L22: 6.5321 REMARK 3 L33: 4.7702 L12: -0.8477 REMARK 3 L13: -1.0844 L23: -2.8230 REMARK 3 S TENSOR REMARK 3 S11: 0.1537 S12: 0.5463 S13: 0.2025 REMARK 3 S21: -0.6024 S22: 0.0200 S23: 0.5401 REMARK 3 S31: 0.4647 S32: -0.2898 S33: -0.1951 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 262:333) REMARK 3 ORIGIN FOR THE GROUP (A): 3.3024 7.1827 -2.1997 REMARK 3 T TENSOR REMARK 3 T11: 0.5074 T22: 0.7217 REMARK 3 T33: 0.4032 T12: -0.1765 REMARK 3 T13: 0.0666 T23: -0.1699 REMARK 3 L TENSOR REMARK 3 L11: 1.1456 L22: 4.8399 REMARK 3 L33: 3.7942 L12: 1.2985 REMARK 3 L13: -1.1758 L23: -2.0624 REMARK 3 S TENSOR REMARK 3 S11: -0.4749 S12: 0.7971 S13: -0.3609 REMARK 3 S21: -1.2033 S22: 0.5890 S23: -0.3559 REMARK 3 S31: 0.4763 S32: -0.1231 S33: -0.1331 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 4M9N 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_1000081640. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JAN-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) : 2.275 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.24500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 48.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 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 39.60750 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: 4810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19390 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 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 465 ALA A 286 REMARK 465 LEU A 287 REMARK 465 GLU A 288 REMARK 465 LYS A 289 REMARK 465 GLY A 290 REMARK 465 PHE A 291 REMARK 465 GLY A 302 REMARK 465 VAL A 303 REMARK 465 THR A 304 REMARK 465 GLY A 305 REMARK 465 VAL A 306 REMARK 465 ALA A 307 REMARK 465 ILE A 323 REMARK 465 GLN A 324 REMARK 465 TRP A 325 REMARK 465 LYS A 326 REMARK 465 TYR A 327 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 CD CE NZ REMARK 470 LYS A 81 CE NZ REMARK 470 LYS A 84 CD CE NZ REMARK 470 GLN A 90 CD OE1 NE2 REMARK 470 GLU A 123 CG CD OE1 OE2 REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 LYS A 220 CD CE NZ REMARK 470 GLU A 232 CG CD OE1 OE2 REMARK 470 GLU A 249 OE1 OE2 REMARK 470 LYS A 262 CD CE NZ REMARK 470 ILE A 277 CG1 CG2 CD1 REMARK 470 LYS A 280 CG CD CE NZ REMARK 470 ARG A 283 NE CZ NH1 NH2 REMARK 470 HIS A 285 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 293 CD1 REMARK 470 LYS A 295 CG CD CE NZ REMARK 470 ARG A 299 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 309 CG CD OE1 OE2 REMARK 470 ASP A 314 OD1 OD2 REMARK 470 LYS A 317 CD CE NZ REMARK 470 ILE A 319 CD1 REMARK 470 ARG A 328 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 329 CG CD OE1 OE2 REMARK 470 LYS A 331 CG CD CE NZ 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. = 2.1 DEGREES REMARK 500 DC T 8 O4' - C1' - N1 ANGL. DEV. = 2.1 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 PRO A 50 44.50 -87.91 REMARK 500 CYS A 178 -145.53 -100.34 REMARK 500 ARG A 333 47.46 -100.37 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 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 84.9 REMARK 620 3 VAL A 65 O 86.4 90.5 REMARK 620 4 HOH A 608 O 92.3 89.3 178.6 REMARK 620 5 DC D 3 OP1 176.1 91.2 94.3 87.1 REMARK 620 6 HOH D 102 O 96.6 177.3 87.4 92.8 87.3 REMARK 620 N 1 2 3 4 5 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 THR A 101 O REMARK 620 2 VAL A 103 O 94.7 REMARK 620 3 ILE A 106 O 95.7 87.7 REMARK 620 4 HOH A 504 O 81.0 93.0 176.7 REMARK 620 5 DG P 9 OP1 162.6 96.7 97.7 85.4 REMARK 620 6 HOH P 101 O 79.0 171.2 86.7 92.2 90.8 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 88.1 REMARK 620 3 DTP A 404 O2A 106.3 100.9 REMARK 620 4 DTP A 404 O2B 146.0 122.9 82.9 REMARK 620 5 DTP A 404 O2G 81.0 165.9 90.8 66.0 REMARK 620 6 HOH A 617 O 62.6 71.8 52.7 135.6 110.3 REMARK 620 7 HOH A 618 O 83.1 101.3 156.2 77.8 68.7 144.8 REMARK 620 N 1 2 3 4 5 6 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 MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTP A 404 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: 4M9J RELATED DB: PDB REMARK 900 RELATED ID: 4M9L RELATED DB: PDB DBREF 4M9N A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 4M9N T 1 16 PDB 4M9N 4M9N 1 16 DBREF 4M9N P 1 10 PDB 4M9N 4M9N 1 10 DBREF 4M9N D 1 5 PDB 4M9N 4M9N 1 5 SEQADV 4M9N 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 MG A 403 1 HET DTP A 404 30 HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE FORMUL 5 NA 2(NA 1+) FORMUL 7 MG MG 2+ FORMUL 8 DTP C10 H16 N5 O12 P3 FORMUL 9 HOH *234(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 HIS A 285 1 11 HELIX 18 18 SER A 315 TYR A 322 1 8 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 LINK O LYS A 60 NA NA A 402 1555 1555 2.44 LINK O LEU A 62 NA NA A 402 1555 1555 2.65 LINK O VAL A 65 NA NA A 402 1555 1555 2.49 LINK O THR A 101 NA NA A 401 1555 1555 2.36 LINK O VAL A 103 NA NA A 401 1555 1555 2.52 LINK O ILE A 106 NA NA A 401 1555 1555 2.38 LINK OD1 ASP A 190 MG MG A 403 1555 1555 2.41 LINK OD2AASP A 192 MG MG A 403 1555 1555 2.36 LINK NA NA A 401 O HOH A 504 1555 1555 2.79 LINK NA NA A 401 OP1 DG P 9 1555 1555 2.36 LINK NA NA A 401 O HOH P 101 1555 1555 2.57 LINK NA NA A 402 O HOH A 608 1555 1555 2.58 LINK NA NA A 402 OP1 DC D 3 1555 1555 2.72 LINK NA NA A 402 O HOH D 102 1555 1555 2.50 LINK MG MG A 403 O2A DTP A 404 1555 1555 2.07 LINK MG MG A 403 O2B DTP A 404 1555 1555 2.10 LINK MG MG A 403 O2G DTP A 404 1555 1555 2.90 LINK MG MG A 403 O HOH A 617 1555 1555 2.92 LINK MG MG A 403 O HOH A 618 1555 1555 2.43 CISPEP 1 GLY A 274 SER A 275 0 2.73 SITE 1 AC1 6 THR A 101 VAL A 103 ILE A 106 HOH A 504 SITE 2 AC1 6 DG P 9 HOH P 101 SITE 1 AC2 6 LYS A 60 LEU A 62 VAL A 65 HOH A 608 SITE 2 AC2 6 DC D 3 HOH D 102 SITE 1 AC3 5 ASP A 190 ASP A 192 DTP A 404 HOH A 617 SITE 2 AC3 5 HOH A 618 SITE 1 AC4 17 ARG A 149 SER A 180 ARG A 183 GLY A 189 SITE 2 AC4 17 ASP A 190 ASP A 192 TYR A 271 PHE A 272 SITE 3 AC4 17 THR A 273 GLY A 274 ASP A 276 ASN A 279 SITE 4 AC4 17 MG A 403 HOH A 603 HOH A 617 HOH A 618 SITE 5 AC4 17 DC P 10 CRYST1 54.523 79.215 54.685 90.00 106.24 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018341 0.000000 0.005341 0.00000 SCALE2 0.000000 0.012624 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019046 0.00000