HEADER HYDROLASE,TRANSFERASE 13-OCT-11 3U7E TITLE CRYSTAL STRUCTURE OF MPNKP CATALYTIC FRAGMENT (D170A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: DNA 5'-KINASE/3'-PHOSPHATASE, POLYNUCLEOTIDE KINASE-3'- COMPND 5 PHOSPHATASE, POLYNUCLEOTIDE 3'-PHOSPHATASE, 2'(3')-POLYNUCLEOTIDASE, COMPND 6 POLYNUCLEOTIDE 5'-HYDROXYL-KINASE; COMPND 7 EC: 3.1.3.32, 2.7.1.78; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PNKP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET19 KEYWDS PROTEIN-DNA COMPLEX, HAD FAMILY, PNKP, DNA REPAIR, PHOSPHATASE, KEYWDS 2 HYDROLASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.COQUELLE,Z.HAVALI,N.BERNSTEIN,R.GREEN,J.N.M.GLOVER REVDAT 5 06-DEC-23 3U7E 1 REMARK REVDAT 4 13-SEP-23 3U7E 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3U7E 1 JRNL REMARK REVDAT 2 29-AUG-12 3U7E 1 JRNL REVDAT 1 14-DEC-11 3U7E 0 JRNL AUTH N.COQUELLE,Z.HAVALI-SHAHRIARI,N.BERNSTEIN,R.GREEN,J.N.GLOVER JRNL TITL STRUCTURAL BASIS FOR THE PHOSPHATASE ACTIVITY OF JRNL TITL 2 POLYNUCLEOTIDE KINASE/PHOSPHATASE ON SINGLE- AND JRNL TITL 3 DOUBLE-STRANDED DNA SUBSTRATES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 21022 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 22171004 JRNL DOI 10.1073/PNAS.1112036108 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.K.BERNSTEIN,R.S.WILLIAMS,M.L.RAKOVSZKY,D.CUI,R.GREEN, REMARK 1 AUTH 2 F.KARIMI-BUSHERI,R.S.MANI,S.GALICIA,C.A.KOCH,C.E.CASS, REMARK 1 AUTH 3 D.DUROCHER,M.WEINFELD,J.N.GLOVER REMARK 1 TITL THE MOLECULAR ARCHITECTURE OF THE MAMMALIAN DNA REPAIR REMARK 1 TITL 2 ENZYME, POLYNUCLEOTIDE KINASE. REMARK 1 REF MOL. CELL V. 17 657 2005 REMARK 1 REFN ISSN 1097-2765 REMARK 1 PMID 15749016 REMARK 1 DOI 10.1016/J.MOLCEL.2005.02.012 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : -3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 39992 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 46.3340 - 4.0966 1.00 2789 147 0.1564 0.1828 REMARK 3 2 4.0966 - 3.2518 1.00 2733 144 0.1454 0.1555 REMARK 3 3 3.2518 - 2.8409 1.00 2712 141 0.1565 0.1985 REMARK 3 4 2.8409 - 2.5811 1.00 2735 144 0.1676 0.2077 REMARK 3 5 2.5811 - 2.3961 1.00 2697 142 0.1590 0.2020 REMARK 3 6 2.3961 - 2.2549 1.00 2707 143 0.1548 0.1904 REMARK 3 7 2.2549 - 2.1419 1.00 2711 143 0.1540 0.2289 REMARK 3 8 2.1419 - 2.0487 1.00 2707 142 0.1568 0.1939 REMARK 3 9 2.0487 - 1.9698 1.00 2720 143 0.1596 0.1933 REMARK 3 10 1.9698 - 1.9019 1.00 2688 142 0.1723 0.1975 REMARK 3 11 1.9019 - 1.8424 1.00 2679 141 0.1856 0.2419 REMARK 3 12 1.8424 - 1.7897 1.00 2704 142 0.1813 0.2193 REMARK 3 13 1.7897 - 1.7426 1.00 2722 143 0.1963 0.2381 REMARK 3 14 1.7426 - 1.7001 1.00 2689 142 0.2163 0.2583 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 42.26 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.23550 REMARK 3 B22 (A**2) : 3.78860 REMARK 3 B33 (A**2) : -2.55310 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.73970 REMARK 3 B23 (A**2) : 0.00000 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 : 0.009 3124 REMARK 3 ANGLE : 1.160 4250 REMARK 3 CHIRALITY : 0.069 460 REMARK 3 PLANARITY : 0.007 554 REMARK 3 DIHEDRAL : 13.827 1171 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 142:217) REMARK 3 ORIGIN FOR THE GROUP (A): 17.9338 15.6921 14.8510 REMARK 3 T TENSOR REMARK 3 T11: 0.0832 T22: 0.0494 REMARK 3 T33: 0.0784 T12: -0.0021 REMARK 3 T13: 0.0080 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.8121 L22: 0.6851 REMARK 3 L33: 1.1179 L12: 0.2952 REMARK 3 L13: 0.3171 L23: 0.0181 REMARK 3 S TENSOR REMARK 3 S11: 0.0224 S12: -0.0833 S13: 0.0656 REMARK 3 S21: 0.0515 S22: 0.0037 S23: 0.0542 REMARK 3 S31: -0.0656 S32: -0.0293 S33: -0.0017 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 218:242) REMARK 3 ORIGIN FOR THE GROUP (A): 10.7778 23.8416 12.9381 REMARK 3 T TENSOR REMARK 3 T11: 0.1496 T22: 0.0913 REMARK 3 T33: 0.1297 T12: 0.0351 REMARK 3 T13: 0.0008 T23: -0.0325 REMARK 3 L TENSOR REMARK 3 L11: 0.3322 L22: 0.4221 REMARK 3 L33: 0.3097 L12: 0.0994 REMARK 3 L13: -0.2008 L23: -0.1274 REMARK 3 S TENSOR REMARK 3 S11: 0.0328 S12: -0.0521 S13: -0.0094 REMARK 3 S21: -0.0137 S22: -0.0531 S23: 0.2178 REMARK 3 S31: -0.1869 S32: -0.2290 S33: 0.0040 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 243:316) REMARK 3 ORIGIN FOR THE GROUP (A): 15.5179 10.4850 4.9420 REMARK 3 T TENSOR REMARK 3 T11: 0.0875 T22: 0.0505 REMARK 3 T33: 0.0937 T12: -0.0045 REMARK 3 T13: 0.0117 T23: 0.0049 REMARK 3 L TENSOR REMARK 3 L11: 0.8398 L22: 1.1729 REMARK 3 L33: 1.2590 L12: -0.4232 REMARK 3 L13: 0.6098 L23: 0.4843 REMARK 3 S TENSOR REMARK 3 S11: 0.0021 S12: -0.0416 S13: -0.0779 REMARK 3 S21: 0.0498 S22: -0.0051 S23: 0.1247 REMARK 3 S31: 0.0620 S32: -0.0629 S33: -0.0054 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 317:341) REMARK 3 ORIGIN FOR THE GROUP (A): 12.6388 -0.4149 8.1937 REMARK 3 T TENSOR REMARK 3 T11: 0.1557 T22: -0.2175 REMARK 3 T33: 0.2136 T12: -0.0642 REMARK 3 T13: -0.0264 T23: 0.0635 REMARK 3 L TENSOR REMARK 3 L11: 0.6045 L22: 0.0990 REMARK 3 L33: 1.3711 L12: -0.1169 REMARK 3 L13: 0.4741 L23: 0.1644 REMARK 3 S TENSOR REMARK 3 S11: 0.1135 S12: -0.0484 S13: -0.6015 REMARK 3 S21: 0.0544 S22: 0.0298 S23: 0.3374 REMARK 3 S31: 0.7010 S32: -0.2600 S33: 0.1435 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 342:384) REMARK 3 ORIGIN FOR THE GROUP (A): -0.5010 7.7145 -28.1488 REMARK 3 T TENSOR REMARK 3 T11: 0.1439 T22: 0.2041 REMARK 3 T33: 0.1513 T12: 0.0226 REMARK 3 T13: -0.0271 T23: -0.0058 REMARK 3 L TENSOR REMARK 3 L11: 0.0409 L22: -0.0207 REMARK 3 L33: 0.8547 L12: -0.0172 REMARK 3 L13: 0.2215 L23: -0.0258 REMARK 3 S TENSOR REMARK 3 S11: 0.0475 S12: 0.0890 S13: -0.0634 REMARK 3 S21: 0.0503 S22: 0.0630 S23: -0.1129 REMARK 3 S31: 0.0874 S32: 0.3600 S33: 0.0388 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 385:466) REMARK 3 ORIGIN FOR THE GROUP (A): -10.1218 14.3559 -26.7764 REMARK 3 T TENSOR REMARK 3 T11: 0.1436 T22: 0.1861 REMARK 3 T33: 0.1338 T12: 0.0338 REMARK 3 T13: -0.0000 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 0.7665 L22: 0.2420 REMARK 3 L33: 1.2199 L12: 0.3617 REMARK 3 L13: 0.7591 L23: 0.1677 REMARK 3 S TENSOR REMARK 3 S11: -0.1141 S12: -0.2877 S13: 0.2673 REMARK 3 S21: 0.0316 S22: -0.0130 S23: 0.0893 REMARK 3 S31: -0.2534 S32: -0.4488 S33: -0.0753 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 467:484) REMARK 3 ORIGIN FOR THE GROUP (A): -6.1330 14.7392 -11.1354 REMARK 3 T TENSOR REMARK 3 T11: 0.1101 T22: 0.4091 REMARK 3 T33: 0.1330 T12: -0.0107 REMARK 3 T13: 0.0469 T23: 0.0235 REMARK 3 L TENSOR REMARK 3 L11: 0.9644 L22: 0.5711 REMARK 3 L33: 0.1816 L12: -0.2568 REMARK 3 L13: -0.0811 L23: -0.2189 REMARK 3 S TENSOR REMARK 3 S11: 0.1138 S12: -0.2195 S13: 0.3075 REMARK 3 S21: 0.0760 S22: -0.1454 S23: -0.0924 REMARK 3 S31: -0.1260 S32: -0.4856 S33: -0.0438 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 485:522) REMARK 3 ORIGIN FOR THE GROUP (A): 2.4484 6.3883 -19.8141 REMARK 3 T TENSOR REMARK 3 T11: 0.1339 T22: 0.2018 REMARK 3 T33: 0.1416 T12: -0.0314 REMARK 3 T13: 0.0039 T23: -0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.2838 L22: 0.2723 REMARK 3 L33: 0.4848 L12: -0.1010 REMARK 3 L13: 0.2866 L23: 0.1540 REMARK 3 S TENSOR REMARK 3 S11: 0.1084 S12: 0.2123 S13: -0.1643 REMARK 3 S21: -0.0419 S22: 0.1140 S23: -0.0796 REMARK 3 S31: 0.2307 S32: 0.0721 S33: 0.0319 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 3U7E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068399. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40013 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 46.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.53400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.780 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1YJ5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, PH 7, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 31.59500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLU B 506 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 B 150 CG CD CE NZ REMARK 470 GLN B 402 CG CD OE1 NE2 REMARK 470 ARG B 432 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 483 CG CD CE NZ REMARK 470 GLN B 505 CB CG CD OE1 NE2 REMARK 470 HIS B 507 CB CG ND1 CD2 CE1 NE2 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 HD1 HIS B 458 HO1 GOL B 524 1.14 REMARK 500 HG1 THR B 344 O HOH B 839 1.55 REMARK 500 O2 GOL B 527 O HOH B 698 1.96 REMARK 500 O PRO B 350 NH1 ARG B 503 1.98 REMARK 500 O HOH B 808 O HOH B 811 2.07 REMARK 500 O HOH B 129 O HOH B 757 2.16 REMARK 500 O HOH B 590 O HOH B 664 2.17 REMARK 500 OD2 ASP B 426 OG SER B 429 2.17 REMARK 500 O HOH B 140 O HOH B 557 2.18 REMARK 500 O HOH B 677 O HOH B 762 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 B 778 O HOH B 789 2545 2.11 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 LEU B 171 -67.08 -104.34 REMARK 500 THR B 174 -55.58 -126.43 REMARK 500 ARG B 300 68.10 -111.97 REMARK 500 ASP B 421 78.65 -106.64 REMARK 500 LEU B 508 150.98 -41.50 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 MG B 523 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PO4 B 1 O3 REMARK 620 2 ASP B 172 O 102.6 REMARK 620 3 ASP B 288 OD1 157.4 80.9 REMARK 620 4 HOH B 834 O 76.4 153.8 90.6 REMARK 620 5 HOH B 835 O 115.5 71.5 86.9 133.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 523 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 524 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 525 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 526 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 527 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 528 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YJ5 RELATED DB: PDB DBREF 3U7E B 142 522 UNP Q9JLV6 PNKP_MOUSE 142 522 SEQADV 3U7E ALA B 170 UNP Q9JLV6 ASP 170 ENGINEERED MUTATION SEQRES 1 B 381 SER SER LEU GLY TRP GLU SER LEU LYS LYS LEU LEU VAL SEQRES 2 B 381 PHE THR ALA SER GLY VAL LYS PRO GLN GLY LYS VAL ALA SEQRES 3 B 381 ALA PHE ALA LEU ASP GLY THR LEU ILE THR THR ARG SER SEQRES 4 B 381 GLY LYS VAL PHE PRO THR SER PRO SER ASP TRP ARG ILE SEQRES 5 B 381 LEU TYR PRO GLU ILE PRO LYS LYS LEU GLN GLU LEU ALA SEQRES 6 B 381 ALA GLU GLY TYR LYS LEU VAL ILE PHE THR ASN GLN MSE SEQRES 7 B 381 GLY ILE GLY ARG GLY LYS LEU PRO ALA GLU VAL PHE LYS SEQRES 8 B 381 GLY LYS VAL GLU ALA VAL LEU GLU LYS LEU GLY VAL PRO SEQRES 9 B 381 PHE GLN VAL LEU VAL ALA THR HIS ALA GLY LEU ASN ARG SEQRES 10 B 381 LYS PRO VAL SER GLY MSE TRP ASP HIS LEU GLN GLU GLN SEQRES 11 B 381 ALA ASN GLU GLY ILE PRO ILE SER VAL GLU ASP SER VAL SEQRES 12 B 381 PHE VAL GLY ASP ALA ALA GLY ARG LEU ALA ASN TRP ALA SEQRES 13 B 381 PRO GLY ARG LYS LYS LYS ASP PHE SER CYS ALA ASP ARG SEQRES 14 B 381 LEU PHE ALA LEU ASN VAL GLY LEU PRO PHE ALA THR PRO SEQRES 15 B 381 GLU GLU PHE PHE LEU LYS TRP PRO ALA ALA ARG PHE GLU SEQRES 16 B 381 LEU PRO ALA PHE ASP PRO ARG THR ILE SER SER ALA GLY SEQRES 17 B 381 PRO LEU TYR LEU PRO GLU SER SER SER LEU LEU SER PRO SEQRES 18 B 381 ASN PRO GLU VAL VAL VAL ALA VAL GLY PHE PRO GLY ALA SEQRES 19 B 381 GLY LYS SER THR PHE ILE GLN GLU HIS LEU VAL SER ALA SEQRES 20 B 381 GLY TYR VAL HIS VAL ASN ARG ASP THR LEU GLY SER TRP SEQRES 21 B 381 GLN ARG CYS VAL SER SER CYS GLN ALA ALA LEU ARG GLN SEQRES 22 B 381 GLY LYS ARG VAL VAL ILE ASP ASN THR ASN PRO ASP VAL SEQRES 23 B 381 PRO SER ARG ALA ARG TYR ILE GLN CYS ALA LYS ASP ALA SEQRES 24 B 381 GLY VAL PRO CYS ARG CYS PHE ASN PHE CSO ALA THR ILE SEQRES 25 B 381 GLU GLN ALA ARG HIS ASN ASN ARG PHE ARG GLU MSE THR SEQRES 26 B 381 ASP PRO SER HIS ALA PRO VAL SER ASP MSE VAL MSE PHE SEQRES 27 B 381 SER TYR ARG LYS GLN PHE GLU PRO PRO THR LEU ALA GLU SEQRES 28 B 381 GLY PHE LEU GLU ILE LEU GLU ILE PRO PHE ARG LEU GLN SEQRES 29 B 381 GLU HIS LEU ASP PRO ALA LEU GLN ARG LEU TYR ARG GLN SEQRES 30 B 381 PHE SER GLU GLY MODRES 3U7E MSE B 219 MET SELENOMETHIONINE MODRES 3U7E MSE B 264 MET SELENOMETHIONINE MODRES 3U7E CSO B 450 CYS S-HYDROXYCYSTEINE MODRES 3U7E MSE B 465 MET SELENOMETHIONINE MODRES 3U7E MSE B 476 MET SELENOMETHIONINE MODRES 3U7E MSE B 478 MET SELENOMETHIONINE HET MSE B 219 31 HET MSE B 264 17 HET CSO B 450 12 HET MSE B 465 17 HET MSE B 476 17 HET MSE B 478 17 HET PO4 B 1 5 HET MG B 523 1 HET GOL B 524 14 HET GOL B 525 14 HET GOL B 526 14 HET GOL B 527 14 HET GOL B 528 14 HETNAM MSE SELENOMETHIONINE HETNAM CSO S-HYDROXYCYSTEINE HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 PO4 O4 P 3- FORMUL 3 MG MG 2+ FORMUL 4 GOL 5(C3 H8 O3) FORMUL 9 HOH *451(H2 O) HELIX 1 1 GLU B 197 GLU B 208 1 12 HELIX 2 2 GLN B 218 ARG B 223 1 6 HELIX 3 3 PRO B 227 GLY B 243 1 17 HELIX 4 4 SER B 262 ALA B 272 1 11 HELIX 5 5 CYS B 307 GLY B 317 1 11 HELIX 6 6 THR B 322 LYS B 329 1 8 HELIX 7 7 ASP B 341 ILE B 345 5 5 HELIX 8 8 GLY B 376 LEU B 385 1 10 HELIX 9 9 VAL B 386 GLY B 389 5 4 HELIX 10 10 ASN B 394 GLY B 399 1 6 HELIX 11 11 SER B 400 GLN B 414 1 15 HELIX 12 12 ASP B 426 GLY B 441 1 16 HELIX 13 13 THR B 452 ASP B 467 1 16 HELIX 14 14 SER B 474 PHE B 485 1 12 HELIX 15 15 THR B 489 GLY B 493 5 5 HELIX 16 16 ASP B 509 ARG B 517 1 9 SHEET 1 A 7 GLY B 145 LEU B 149 0 SHEET 2 A 7 LEU B 152 THR B 156 -1 O LEU B 152 N LEU B 149 SHEET 3 A 7 GLN B 247 ALA B 251 -1 O VAL B 248 N PHE B 155 SHEET 4 A 7 LYS B 211 ASN B 217 1 N ILE B 214 O LEU B 249 SHEET 5 A 7 VAL B 166 PHE B 169 1 N ALA B 167 O LYS B 211 SHEET 6 A 7 VAL B 284 VAL B 286 1 O VAL B 284 N ALA B 168 SHEET 7 A 7 PHE B 320 ALA B 321 1 O ALA B 321 N PHE B 285 SHEET 1 B 2 ILE B 176 THR B 177 0 SHEET 2 B 2 ARG B 192 ILE B 193 -1 O ARG B 192 N THR B 177 SHEET 1 C 5 VAL B 391 VAL B 393 0 SHEET 2 C 5 VAL B 418 ILE B 420 1 O VAL B 419 N VAL B 391 SHEET 3 C 5 VAL B 366 VAL B 370 1 N VAL B 367 O ILE B 420 SHEET 4 C 5 CYS B 444 PHE B 449 1 O PHE B 449 N VAL B 370 SHEET 5 C 5 GLU B 496 ILE B 500 1 O LEU B 498 N ASN B 448 LINK C GLN B 218 N MSE B 219 1555 1555 1.33 LINK C MSE B 219 N GLY B 220 1555 1555 1.33 LINK C GLY B 263 N MSE B 264 1555 1555 1.33 LINK C MSE B 264 N TRP B 265 1555 1555 1.33 LINK C PHE B 449 N CSO B 450 1555 1555 1.34 LINK C CSO B 450 N ALA B 451 1555 1555 1.32 LINK C GLU B 464 N MSE B 465 1555 1555 1.33 LINK C MSE B 465 N THR B 466 1555 1555 1.33 LINK C ASP B 475 N MSE B 476 1555 1555 1.34 LINK C MSE B 476 N VAL B 477 1555 1555 1.33 LINK C VAL B 477 N MSE B 478 1555 1555 1.34 LINK C MSE B 478 N APHE B 479 1555 1555 1.33 LINK C MSE B 478 N BPHE B 479 1555 1555 1.33 LINK O3 PO4 B 1 MG MG B 523 1555 1555 2.10 LINK O ASP B 172 MG MG B 523 1555 1555 2.12 LINK OD1 ASP B 288 MG MG B 523 1555 1555 2.23 LINK MG MG B 523 O HOH B 834 1555 1555 2.02 LINK MG MG B 523 O HOH B 835 1555 1555 2.89 CISPEP 1 LYS B 259 PRO B 260 0 11.08 CISPEP 2 LEU B 353 PRO B 354 0 -2.26 SITE 1 AC1 10 HOH B 103 LEU B 171 ASP B 172 THR B 216 SITE 2 AC1 10 ASN B 217 GLN B 218 LYS B 259 MG B 523 SITE 3 AC1 10 HOH B 693 HOH B 834 SITE 1 AC2 5 PO4 B 1 ASP B 172 ASP B 288 HOH B 834 SITE 2 AC2 5 HOH B 835 SITE 1 AC3 8 PRO B 338 PHE B 340 HIS B 458 ARG B 461 SITE 2 AC3 8 PHE B 519 SER B 520 GLU B 521 HOH B 840 SITE 1 AC4 9 HOH B 41 GLY B 159 VAL B 160 LYS B 161 SITE 2 AC4 9 GLN B 163 TYR B 210 LYS B 211 LEU B 212 SITE 3 AC4 9 HOH B 561 SITE 1 AC5 8 HOH B 31 ARG B 310 PHE B 320 GLU B 325 SITE 2 AC5 8 ALA B 332 PHE B 335 HOH B 635 HOH B 697 SITE 1 AC6 7 LYS B 201 LEU B 205 GLU B 208 TYR B 210 SITE 2 AC6 7 PHE B 326 HOH B 675 HOH B 698 SITE 1 AC7 10 HOH B 67 PHE B 372 PRO B 373 GLY B 374 SITE 2 AC7 10 ALA B 375 GLY B 376 LYS B 377 SER B 378 SITE 3 AC7 10 HOH B 571 HOH B 763 CRYST1 42.820 63.190 68.120 90.00 88.23 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 0.023354 0.000000 -0.000721 0.00000 SCALE2 0.000000 0.015825 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014687 0.00000