HEADER HYDROLASE,TRANSFERASE/DNA 13-OCT-11 3U7H TITLE CRYSTAL STRUCTURE OF MPNKP CATALYTIC FRAGMENT (D170A) BOUND TO SINGLE- TITLE 2 STRANDED DNA (TCCTTP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: UNP RESIDUES 142-522; COMPND 5 SYNONYM: DNA 5'-KINASE/3'-PHOSPHATASE, POLYNUCLEOTIDE KINASE-3'- COMPND 6 PHOSPHATASE, POLYNUCLEOTIDE 3'-PHOSPHATASE, 2'(3')-POLYNUCLEOTIDASE, COMPND 7 POLYNUCLEOTIDE 5'-HYDROXYL-KINASE; COMPND 8 EC: 3.1.3.32, 2.7.1.78; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: DNA; COMPND 13 CHAIN: X; COMPND 14 ENGINEERED: 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; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: DNA SUBSTRATE OF PNKP PHOSPHATASE DOMAIN KEYWDS PROTEIN-DNA COMPLEX, HAD FAMILY, PNKP, DNA REPAIR, PHOSPHATASE, KEYWDS 2 HYDROLASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.COQUELLE,Z.HAVALI,N.BERNSTEIN,R.GREEN,J.N.M.GLOVER REVDAT 3 08-NOV-17 3U7H 1 JRNL REMARK REVDAT 2 29-AUG-12 3U7H 1 JRNL REVDAT 1 14-DEC-11 3U7H 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. 2.00 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : -3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 23527 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1176 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 31.0380 - 3.9974 0.95 2807 148 0.1667 0.1745 REMARK 3 2 3.9974 - 3.1739 0.97 2838 150 0.1635 0.2389 REMARK 3 3 3.1739 - 2.7729 0.99 2874 151 0.1880 0.2204 REMARK 3 4 2.7729 - 2.5195 0.99 2820 149 0.2045 0.2703 REMARK 3 5 2.5195 - 2.3390 0.98 2839 149 0.2171 0.2605 REMARK 3 6 2.3390 - 2.2012 0.96 2752 145 0.2189 0.2995 REMARK 3 7 2.2012 - 2.0909 0.96 2759 145 0.2305 0.2748 REMARK 3 8 2.0909 - 1.9999 0.93 2662 139 0.2555 0.2955 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 38.77 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.570 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.13020 REMARK 3 B22 (A**2) : 2.42280 REMARK 3 B33 (A**2) : -3.55290 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.35220 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 3030 REMARK 3 ANGLE : 1.005 4116 REMARK 3 CHIRALITY : 0.056 451 REMARK 3 PLANARITY : 0.004 531 REMARK 3 DIHEDRAL : 15.164 1117 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 144:217) REMARK 3 ORIGIN FOR THE GROUP (A): 2.4843 -16.1367 48.5908 REMARK 3 T TENSOR REMARK 3 T11: 0.0750 T22: 0.0605 REMARK 3 T33: 0.0706 T12: -0.0021 REMARK 3 T13: 0.0017 T23: -0.0126 REMARK 3 L TENSOR REMARK 3 L11: 1.2839 L22: 0.9291 REMARK 3 L33: 1.1297 L12: 0.2290 REMARK 3 L13: -0.0942 L23: -0.1470 REMARK 3 S TENSOR REMARK 3 S11: 0.0553 S12: -0.0957 S13: -0.0394 REMARK 3 S21: 0.0893 S22: -0.0093 S23: -0.0473 REMARK 3 S31: 0.1129 S32: -0.0531 S33: -0.0513 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 218:242) REMARK 3 ORIGIN FOR THE GROUP (A): 9.4710 -24.5313 47.3743 REMARK 3 T TENSOR REMARK 3 T11: 0.1757 T22: 0.1236 REMARK 3 T33: 0.1522 T12: 0.0184 REMARK 3 T13: -0.0176 T23: 0.0215 REMARK 3 L TENSOR REMARK 3 L11: 1.8527 L22: 2.4434 REMARK 3 L33: 1.9963 L12: -0.9135 REMARK 3 L13: -0.6474 L23: 0.9124 REMARK 3 S TENSOR REMARK 3 S11: 0.0319 S12: -0.1818 S13: -0.0541 REMARK 3 S21: 0.0270 S22: -0.1067 S23: -0.1882 REMARK 3 S31: 0.2248 S32: 0.2772 S33: 0.0932 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 243:316) REMARK 3 ORIGIN FOR THE GROUP (A): 4.5650 -11.3377 38.6125 REMARK 3 T TENSOR REMARK 3 T11: 0.0755 T22: 0.0778 REMARK 3 T33: 0.0874 T12: 0.0047 REMARK 3 T13: -0.0052 T23: -0.0136 REMARK 3 L TENSOR REMARK 3 L11: 1.2188 L22: 1.3341 REMARK 3 L33: 1.0223 L12: -0.1155 REMARK 3 L13: -0.7136 L23: -0.5760 REMARK 3 S TENSOR REMARK 3 S11: 0.0292 S12: -0.0492 S13: 0.0397 REMARK 3 S21: 0.0504 S22: -0.0079 S23: -0.0747 REMARK 3 S31: 0.0061 S32: 0.0733 S33: -0.0172 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 317:341) REMARK 3 ORIGIN FOR THE GROUP (A): 7.8021 -0.2771 41.9183 REMARK 3 T TENSOR REMARK 3 T11: 0.1887 T22: 0.0289 REMARK 3 T33: 0.2152 T12: -0.0513 REMARK 3 T13: 0.0094 T23: -0.0356 REMARK 3 L TENSOR REMARK 3 L11: 0.3607 L22: 0.3091 REMARK 3 L33: 1.9482 L12: 0.0975 REMARK 3 L13: -0.4940 L23: -0.0738 REMARK 3 S TENSOR REMARK 3 S11: 0.0984 S12: -0.3265 S13: 0.2614 REMARK 3 S21: -0.0639 S22: -0.1340 S23: -0.1847 REMARK 3 S31: -0.7076 S32: 0.3474 S33: 0.0031 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 342:384) REMARK 3 ORIGIN FOR THE GROUP (A): 20.7444 -8.1414 5.7472 REMARK 3 T TENSOR REMARK 3 T11: 0.1651 T22: 0.2032 REMARK 3 T33: 0.1802 T12: 0.0441 REMARK 3 T13: 0.0140 T23: -0.0105 REMARK 3 L TENSOR REMARK 3 L11: 0.2535 L22: -0.0696 REMARK 3 L33: 1.5548 L12: 0.0148 REMARK 3 L13: -0.7730 L23: -0.0827 REMARK 3 S TENSOR REMARK 3 S11: 0.0422 S12: 0.1648 S13: 0.0738 REMARK 3 S21: 0.0423 S22: 0.1565 S23: 0.1247 REMARK 3 S31: -0.1004 S32: -0.2682 S33: -0.0891 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 385:466) REMARK 3 ORIGIN FOR THE GROUP (A): 29.6934 -14.2513 7.2574 REMARK 3 T TENSOR REMARK 3 T11: 0.1735 T22: 0.2003 REMARK 3 T33: 0.1480 T12: 0.0181 REMARK 3 T13: 0.0075 T23: -0.0492 REMARK 3 L TENSOR REMARK 3 L11: 0.5730 L22: 0.2302 REMARK 3 L33: 1.3857 L12: 0.2686 REMARK 3 L13: -0.4937 L23: -0.5818 REMARK 3 S TENSOR REMARK 3 S11: -0.1362 S12: -0.1139 S13: -0.1639 REMARK 3 S21: 0.0193 S22: 0.0625 S23: -0.0592 REMARK 3 S31: 0.2177 S32: 0.3409 S33: 0.0128 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 467:484) REMARK 3 ORIGIN FOR THE GROUP (A): 26.4625 -15.4846 22.4925 REMARK 3 T TENSOR REMARK 3 T11: 0.2061 T22: 0.3189 REMARK 3 T33: 0.1945 T12: 0.0115 REMARK 3 T13: -0.0115 T23: -0.0608 REMARK 3 L TENSOR REMARK 3 L11: 1.9112 L22: 2.1426 REMARK 3 L33: 1.1163 L12: 0.5565 REMARK 3 L13: -0.4495 L23: -0.2425 REMARK 3 S TENSOR REMARK 3 S11: -0.0045 S12: -0.1367 S13: -0.1615 REMARK 3 S21: 0.4773 S22: 0.0992 S23: 0.0407 REMARK 3 S31: -0.0340 S32: 0.5731 S33: -0.0165 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 485:522) REMARK 3 ORIGIN FOR THE GROUP (A): 18.6595 -7.0383 13.9630 REMARK 3 T TENSOR REMARK 3 T11: 0.2239 T22: 0.1945 REMARK 3 T33: 0.1402 T12: -0.0275 REMARK 3 T13: -0.0107 T23: -0.0194 REMARK 3 L TENSOR REMARK 3 L11: 1.2333 L22: 0.5023 REMARK 3 L33: 1.3537 L12: 0.1788 REMARK 3 L13: -1.1582 L23: -0.5804 REMARK 3 S TENSOR REMARK 3 S11: -0.0031 S12: 0.1823 S13: 0.1576 REMARK 3 S21: -0.1366 S22: 0.1909 S23: 0.0842 REMARK 3 S31: -0.2118 S32: -0.0545 S33: -0.0708 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 3U7H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000068402. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-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 : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23538 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 31.034 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.50600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.850 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% 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 31.26500 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, X 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 GLY B 399 REMARK 465 SER B 400 REMARK 465 TRP B 401 REMARK 465 GLN B 402 REMARK 465 ARG B 403 REMARK 465 GLU B 506 REMARK 465 DT X 523 REMARK 465 DC X 524 REMARK 465 DC X 525 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 PHE B 184 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 300 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 301 CG CD CE NZ REMARK 470 LYS B 302 CG CD CE NZ REMARK 470 ARG B 395 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 507 CG ND1 CD2 CE1 NE2 REMARK 470 DT X 526 P OP1 OP2 N1 C2 O2 N3 REMARK 470 DT X 526 C4 O4 C5 C7 C6 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 612 O HOH B 614 2.07 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 -73.42 -99.69 REMARK 500 ASN B 295 7.96 82.04 REMARK 500 TRP B 296 -0.02 -51.38 REMARK 500 ARG B 300 53.70 -106.02 REMARK 500 ARG B 395 -35.23 -39.98 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 532 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PO4 X 528 O1 REMARK 620 2 ASP B 288 OD1 152.7 REMARK 620 3 ASP B 172 O 87.9 80.6 REMARK 620 4 HOH B 617 O 106.0 96.8 81.9 REMARK 620 5 HOH B 27 O 90.3 100.3 177.6 100.2 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 X 528 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 529 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 530 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 531 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 532 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YJ5 RELATED DB: PDB REMARK 900 RELATED ID: 3U7E RELATED DB: PDB REMARK 900 RELATED ID: 3U7F RELATED DB: PDB REMARK 900 RELATED ID: 3U7G RELATED DB: PDB DBREF 3U7H B 142 522 UNP Q9JLV6 PNKP_MOUSE 142 522 DBREF 3U7H X 523 527 PDB 3U7H 3U7H 523 527 SEQADV 3U7H 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 SEQRES 1 X 5 DT DC DC DT DT MODRES 3U7H MSE B 219 MET SELENOMETHIONINE MODRES 3U7H MSE B 264 MET SELENOMETHIONINE MODRES 3U7H CSO B 450 CYS S-HYDROXYCYSTEINE MODRES 3U7H MSE B 465 MET SELENOMETHIONINE MODRES 3U7H MSE B 476 MET SELENOMETHIONINE MODRES 3U7H MSE B 478 MET SELENOMETHIONINE HET MSE B 219 17 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 GOL B 1 14 HET GOL B 2 14 HET GOL B 529 14 HET GOL B 530 14 HET GOL B 531 14 HET MG B 532 1 HET PO4 X 528 4 HETNAM MSE SELENOMETHIONINE HETNAM CSO S-HYDROXYCYSTEINE HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION 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 3 GOL 5(C3 H8 O3) FORMUL 8 MG MG 2+ FORMUL 9 PO4 O4 P 3- FORMUL 10 HOH *234(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 LEU B 398 5 5 HELIX 11 11 VAL B 405 GLN B 414 1 10 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 THR B 216 O ALA B 251 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 SSBOND 1 CYS B 408 CYS B 436 1555 1555 2.94 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 1.32 LINK C MSE B 264 N TRP B 265 1555 1555 1.33 LINK C PHE B 449 N CSO B 450 1555 1555 1.33 LINK C CSO B 450 N ALA B 451 1555 1555 1.33 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 1.33 LINK C MSE B 476 N VAL B 477 1555 1555 1.33 LINK C VAL B 477 N MSE B 478 1555 1555 1.33 LINK C MSE B 478 N PHE B 479 1555 1555 1.33 LINK O1 PO4 X 528 MG MG B 532 1555 1555 1.85 LINK OD1 ASP B 288 MG MG B 532 1555 1555 2.13 LINK O ASP B 172 MG MG B 532 1555 1555 2.22 LINK MG MG B 532 O HOH B 617 1555 1555 2.06 LINK MG MG B 532 O HOH B 27 1555 1555 2.09 LINK O3' DT X 527 P PO4 X 528 1555 1555 1.61 CISPEP 1 LYS B 259 PRO B 260 0 8.05 CISPEP 2 LEU B 353 PRO B 354 0 -2.64 SITE 1 AC1 9 HOH B 27 LEU B 171 ASP B 172 THR B 216 SITE 2 AC1 9 ASN B 217 LYS B 259 MG B 532 HOH X 46 SITE 3 AC1 9 DT X 527 SITE 1 AC2 8 HOH B 52 PRO B 338 PHE B 340 HIS B 458 SITE 2 AC2 8 ARG B 461 PHE B 519 SER B 520 GLU B 521 SITE 1 AC3 8 HOH B 28 VAL B 160 LYS B 161 GLN B 163 SITE 2 AC3 8 TYR B 210 LYS B 211 LEU B 212 HOH B 544 SITE 1 AC4 5 HOH B 24 ARG B 310 GLU B 325 ALA B 332 SITE 2 AC4 5 PHE B 335 SITE 1 AC5 3 HOH B 38 TYR B 210 PHE B 326 SITE 1 AC6 9 HOH B 95 PHE B 372 PRO B 373 GLY B 374 SITE 2 AC6 9 ALA B 375 GLY B 376 LYS B 377 HOH B 615 SITE 3 AC6 9 HOH B 618 SITE 1 AC7 5 HOH B 27 ASP B 172 ASP B 288 HOH B 617 SITE 2 AC7 5 PO4 X 528 CRYST1 42.830 62.530 67.980 90.00 91.69 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 0.023348 0.000000 0.000691 0.00000 SCALE2 0.000000 0.015992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014717 0.00000