HEADER HYDROLASE,TRANSFERASE/DNA 13-OCT-11 3U7G TITLE CRYSTAL STRUCTURE OF MPNKP CATALYTIC FRAGMENT (D170A) BOUND TO SINGLE- TITLE 2 STRANDED DNA (TCCTAP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE; COMPND 3 CHAIN: A; 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; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: DNA; COMPND 12 CHAIN: X; COMPND 13 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 3U7G 1 REMARK REVDAT 2 29-AUG-12 3U7G 1 JRNL REVDAT 1 14-DEC-11 3U7G 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : -3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 21474 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1082 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 40.5511 - 4.1985 0.97 2827 143 0.1844 0.2147 REMARK 3 2 4.1985 - 3.3329 0.86 2426 131 0.1924 0.2629 REMARK 3 3 3.3329 - 2.9118 0.98 2760 145 0.2169 0.2757 REMARK 3 4 2.9118 - 2.6456 0.87 2430 133 0.2208 0.2597 REMARK 3 5 2.6456 - 2.4560 0.98 2701 140 0.2162 0.2532 REMARK 3 6 2.4560 - 2.3112 0.98 2750 146 0.2242 0.2994 REMARK 3 7 2.3112 - 2.1955 0.76 2134 113 0.2329 0.3135 REMARK 3 8 2.1955 - 2.0999 0.86 2364 131 0.2355 0.2918 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 33.57 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.570 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.08410 REMARK 3 B22 (A**2) : 8.99180 REMARK 3 B33 (A**2) : -1.90770 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.58480 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 3074 REMARK 3 ANGLE : 1.044 4179 REMARK 3 CHIRALITY : 0.055 453 REMARK 3 PLANARITY : 0.005 536 REMARK 3 DIHEDRAL : 13.879 1132 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 144:217) REMARK 3 ORIGIN FOR THE GROUP (A): -1.0291 -2.6612 -46.4129 REMARK 3 T TENSOR REMARK 3 T11: 0.1285 T22: 0.1173 REMARK 3 T33: 0.1570 T12: -0.0283 REMARK 3 T13: -0.0005 T23: -0.0623 REMARK 3 L TENSOR REMARK 3 L11: 0.6009 L22: 0.3128 REMARK 3 L33: 0.5305 L12: -0.1133 REMARK 3 L13: 0.2890 L23: 0.0895 REMARK 3 S TENSOR REMARK 3 S11: -0.0556 S12: 0.2219 S13: -0.3388 REMARK 3 S21: 0.0097 S22: -0.0172 S23: -0.0235 REMARK 3 S31: 0.2073 S32: 0.1310 S33: -0.0568 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 218:242) REMARK 3 ORIGIN FOR THE GROUP (A): -4.5387 -9.2731 -38.6795 REMARK 3 T TENSOR REMARK 3 T11: 0.2288 T22: -0.1306 REMARK 3 T33: 0.2448 T12: 0.0497 REMARK 3 T13: -0.0138 T23: -0.0915 REMARK 3 L TENSOR REMARK 3 L11: 0.1921 L22: 0.2661 REMARK 3 L33: 0.3465 L12: -0.0650 REMARK 3 L13: 0.1515 L23: -0.0007 REMARK 3 S TENSOR REMARK 3 S11: 0.0215 S12: 0.0636 S13: -0.3130 REMARK 3 S21: -0.0076 S22: 0.0816 S23: 0.0147 REMARK 3 S31: 0.3867 S32: 0.0883 S33: 0.2586 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 243:316) REMARK 3 ORIGIN FOR THE GROUP (A): -4.6894 7.0730 -41.9113 REMARK 3 T TENSOR REMARK 3 T11: 0.1078 T22: -0.2463 REMARK 3 T33: 0.0931 T12: -0.0539 REMARK 3 T13: 0.0105 T23: -0.0714 REMARK 3 L TENSOR REMARK 3 L11: 1.8807 L22: 0.5922 REMARK 3 L33: 0.1278 L12: 0.0754 REMARK 3 L13: -0.4335 L23: 0.0146 REMARK 3 S TENSOR REMARK 3 S11: -0.0314 S12: 0.3560 S13: 0.0540 REMARK 3 S21: -0.0393 S22: -0.0214 S23: 0.0292 REMARK 3 S31: -0.1090 S32: -0.0500 S33: 0.0693 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 317:341) REMARK 3 ORIGIN FOR THE GROUP (A): -11.1186 11.8944 -50.1668 REMARK 3 T TENSOR REMARK 3 T11: 0.1296 T22: 0.1978 REMARK 3 T33: 0.1024 T12: 0.0425 REMARK 3 T13: 0.0102 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.5022 L22: 1.2769 REMARK 3 L33: 0.6910 L12: -0.1883 REMARK 3 L13: -0.4246 L23: 0.7857 REMARK 3 S TENSOR REMARK 3 S11: 0.0488 S12: 0.2534 S13: 0.0587 REMARK 3 S21: -0.2076 S22: -0.1181 S23: 0.3176 REMARK 3 S31: -0.3413 S32: -0.4040 S33: -0.0759 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 342:384) REMARK 3 ORIGIN FOR THE GROUP (A): -16.7904 29.6803 -15.8648 REMARK 3 T TENSOR REMARK 3 T11: 0.3463 T22: 0.3798 REMARK 3 T33: 0.1710 T12: 0.1009 REMARK 3 T13: -0.0184 T23: -0.0660 REMARK 3 L TENSOR REMARK 3 L11: 1.3495 L22: 0.0577 REMARK 3 L33: 1.2023 L12: -0.1845 REMARK 3 L13: 0.0025 L23: 0.1013 REMARK 3 S TENSOR REMARK 3 S11: -0.2588 S12: -0.7408 S13: 0.3624 REMARK 3 S21: -0.0762 S22: 0.0303 S23: -0.1380 REMARK 3 S31: -0.6709 S32: -0.0686 S33: -0.2975 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 385:466) REMARK 3 ORIGIN FOR THE GROUP (A): -23.9954 23.1073 -9.6474 REMARK 3 T TENSOR REMARK 3 T11: 0.0318 T22: 0.6996 REMARK 3 T33: -0.8286 T12: 0.1273 REMARK 3 T13: 0.0787 T23: -0.2178 REMARK 3 L TENSOR REMARK 3 L11: 1.2316 L22: 0.2073 REMARK 3 L33: 0.3146 L12: -0.1882 REMARK 3 L13: 0.5934 L23: -0.0466 REMARK 3 S TENSOR REMARK 3 S11: 0.0195 S12: -1.4566 S13: 0.2471 REMARK 3 S21: 0.6998 S22: 0.0866 S23: 0.4243 REMARK 3 S31: -0.2254 S32: -0.7220 S33: 0.4173 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 467:484) REMARK 3 ORIGIN FOR THE GROUP (A): -23.4160 11.5266 -20.9454 REMARK 3 T TENSOR REMARK 3 T11: 0.2707 T22: 0.3938 REMARK 3 T33: 0.3800 T12: 0.0015 REMARK 3 T13: -0.0131 T23: 0.1650 REMARK 3 L TENSOR REMARK 3 L11: 0.3364 L22: 0.2273 REMARK 3 L33: 0.3533 L12: -0.0280 REMARK 3 L13: 0.0980 L23: 0.2675 REMARK 3 S TENSOR REMARK 3 S11: -0.1358 S12: -0.1225 S13: -0.4817 REMARK 3 S21: 0.0969 S22: 0.0269 S23: -0.1600 REMARK 3 S31: 0.5026 S32: 0.0217 S33: -0.0588 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 485:522) REMARK 3 ORIGIN FOR THE GROUP (A): -16.8480 25.0436 -22.7248 REMARK 3 T TENSOR REMARK 3 T11: 0.2336 T22: 0.2325 REMARK 3 T33: 0.2352 T12: 0.0871 REMARK 3 T13: -0.0578 T23: -0.2284 REMARK 3 L TENSOR REMARK 3 L11: 0.4216 L22: 0.2403 REMARK 3 L33: 0.0943 L12: -0.1901 REMARK 3 L13: 0.0900 L23: -0.1314 REMARK 3 S TENSOR REMARK 3 S11: -0.1504 S12: -0.5509 S13: 0.3733 REMARK 3 S21: 0.0588 S22: 0.1280 S23: -0.1363 REMARK 3 S31: -0.3315 S32: -0.3195 S33: -0.0999 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 3U7G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068401. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 12.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1172 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 40.544 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.380 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: 1YJ5 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 (%): 46.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 38.58000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.51500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.58000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.51500 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLU A 506 REMARK 465 HIS A 507 REMARK 465 DT X 398 REMARK 465 DC X 399 REMARK 465 DC X 400 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 ARG A 395 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 402 CG CD OE1 NE2 REMARK 470 GLN A 505 CG CD OE1 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 HO3 GOL A 526 O HOH A 29 1.59 REMARK 500 OE2 GLU A 492 O HOH A 89 1.90 REMARK 500 O PRO A 354 O HOH A 80 2.01 REMARK 500 ND2 ASN A 422 O HOH A 101 2.05 REMARK 500 OG SER A 357 O HOH A 93 2.08 REMARK 500 O GLU A 492 O HOH A 103 2.10 REMARK 500 O ASP A 304 O HOH A 73 2.14 REMARK 500 O HOH A 86 O HOH A 137 2.18 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 A 171 -72.11 -94.74 REMARK 500 THR A 174 -51.83 -127.93 REMARK 500 PRO A 298 123.86 -31.16 REMARK 500 PHE A 372 151.47 -47.47 REMARK 500 THR A 397 -60.12 -94.75 REMARK 500 LEU A 398 -81.13 -53.43 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 A 529 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PO4 X 523 O1 REMARK 620 2 ASP A 172 O 82.2 REMARK 620 3 ASP A 288 OD1 138.2 85.8 REMARK 620 4 ASP A 288 OD2 171.4 92.6 47.4 REMARK 620 5 HOH A 5 O 84.8 165.7 100.2 100.9 REMARK 620 6 HOH A 20 O 111.0 76.7 104.8 61.0 113.7 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 PO4 X 523 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 526 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 527 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 528 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 529 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: 3U7H RELATED DB: PDB DBREF 3U7G A 144 522 UNP Q9JLV6 PNKP_MOUSE 144 522 DBREF 3U7G X 398 402 PDB 3U7G 3U7G 398 402 SEQADV 3U7G ALA A 170 UNP Q9JLV6 ASP 170 ENGINEERED MUTATION SEQRES 1 A 379 LEU GLY TRP GLU SER LEU LYS LYS LEU LEU VAL PHE THR SEQRES 2 A 379 ALA SER GLY VAL LYS PRO GLN GLY LYS VAL ALA ALA PHE SEQRES 3 A 379 ALA LEU ASP GLY THR LEU ILE THR THR ARG SER GLY LYS SEQRES 4 A 379 VAL PHE PRO THR SER PRO SER ASP TRP ARG ILE LEU TYR SEQRES 5 A 379 PRO GLU ILE PRO LYS LYS LEU GLN GLU LEU ALA ALA GLU SEQRES 6 A 379 GLY TYR LYS LEU VAL ILE PHE THR ASN GLN MSE GLY ILE SEQRES 7 A 379 GLY ARG GLY LYS LEU PRO ALA GLU VAL PHE LYS GLY LYS SEQRES 8 A 379 VAL GLU ALA VAL LEU GLU LYS LEU GLY VAL PRO PHE GLN SEQRES 9 A 379 VAL LEU VAL ALA THR HIS ALA GLY LEU ASN ARG LYS PRO SEQRES 10 A 379 VAL SER GLY MSE TRP ASP HIS LEU GLN GLU GLN ALA ASN SEQRES 11 A 379 GLU GLY ILE PRO ILE SER VAL GLU ASP SER VAL PHE VAL SEQRES 12 A 379 GLY ASP ALA ALA GLY ARG LEU ALA ASN TRP ALA PRO GLY SEQRES 13 A 379 ARG LYS LYS LYS ASP PHE SER CYS ALA ASP ARG LEU PHE SEQRES 14 A 379 ALA LEU ASN VAL GLY LEU PRO PHE ALA THR PRO GLU GLU SEQRES 15 A 379 PHE PHE LEU LYS TRP PRO ALA ALA ARG PHE GLU LEU PRO SEQRES 16 A 379 ALA PHE ASP PRO ARG THR ILE SER SER ALA GLY PRO LEU SEQRES 17 A 379 TYR LEU PRO GLU SER SER SER LEU LEU SER PRO ASN PRO SEQRES 18 A 379 GLU VAL VAL VAL ALA VAL GLY PHE PRO GLY ALA GLY LYS SEQRES 19 A 379 SER THR PHE ILE GLN GLU HIS LEU VAL SER ALA GLY TYR SEQRES 20 A 379 VAL HIS VAL ASN ARG ASP THR LEU GLY SER TRP GLN ARG SEQRES 21 A 379 CYS VAL SER SER CYS GLN ALA ALA LEU ARG GLN GLY LYS SEQRES 22 A 379 ARG VAL VAL ILE ASP ASN THR ASN PRO ASP VAL PRO SER SEQRES 23 A 379 ARG ALA ARG TYR ILE GLN CYS ALA LYS ASP ALA GLY VAL SEQRES 24 A 379 PRO CYS ARG CYS PHE ASN PHE CYS ALA THR ILE GLU GLN SEQRES 25 A 379 ALA ARG HIS ASN ASN ARG PHE ARG GLU MSE THR ASP PRO SEQRES 26 A 379 SER HIS ALA PRO VAL SER ASP MSE VAL MSE PHE SER TYR SEQRES 27 A 379 ARG LYS GLN PHE GLU PRO PRO THR LEU ALA GLU GLY PHE SEQRES 28 A 379 LEU GLU ILE LEU GLU ILE PRO PHE ARG LEU GLN GLU HIS SEQRES 29 A 379 LEU ASP PRO ALA LEU GLN ARG LEU TYR ARG GLN PHE SER SEQRES 30 A 379 GLU GLY SEQRES 1 X 5 DT DC DC DT DA MODRES 3U7G MSE A 219 MET SELENOMETHIONINE MODRES 3U7G MSE A 264 MET SELENOMETHIONINE MODRES 3U7G MSE A 465 MET SELENOMETHIONINE MODRES 3U7G MSE A 476 MET SELENOMETHIONINE MODRES 3U7G MSE A 478 MET SELENOMETHIONINE HET MSE A 219 17 HET MSE A 264 17 HET MSE A 465 17 HET MSE A 476 17 HET MSE A 478 17 HET GOL A 1 14 HET GOL A 526 14 HET GOL A 527 14 HET PO4 A 528 5 HET MG A 529 1 HET PO4 X 523 4 HETNAM MSE SELENOMETHIONINE HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 3 GOL 3(C3 H8 O3) FORMUL 6 PO4 2(O4 P 3-) FORMUL 7 MG MG 2+ FORMUL 9 HOH *201(H2 O) HELIX 1 1 GLU A 197 GLU A 208 1 12 HELIX 2 2 GLN A 218 ARG A 223 1 6 HELIX 3 3 PRO A 227 GLY A 243 1 17 HELIX 4 4 SER A 262 ALA A 272 1 11 HELIX 5 5 CYS A 307 GLY A 317 1 11 HELIX 6 6 THR A 322 LYS A 329 1 8 HELIX 7 7 ASP A 341 ILE A 345 5 5 HELIX 8 8 GLY A 376 LEU A 385 1 10 HELIX 9 9 VAL A 386 ALA A 388 5 3 HELIX 10 10 SER A 400 GLN A 414 1 15 HELIX 11 11 ASP A 426 ALA A 440 1 15 HELIX 12 12 THR A 452 ASP A 467 1 16 HELIX 13 13 SER A 474 PHE A 485 1 12 HELIX 14 14 THR A 489 GLY A 493 5 5 HELIX 15 15 ASP A 509 ARG A 517 1 9 SHEET 1 A 7 TRP A 146 LEU A 149 0 SHEET 2 A 7 LEU A 152 THR A 156 -1 O VAL A 154 N GLU A 147 SHEET 3 A 7 GLN A 247 ALA A 251 -1 O VAL A 248 N PHE A 155 SHEET 4 A 7 LYS A 211 ASN A 217 1 N ILE A 214 O LEU A 249 SHEET 5 A 7 VAL A 166 PHE A 169 1 N PHE A 169 O PHE A 215 SHEET 6 A 7 VAL A 284 VAL A 286 1 O VAL A 284 N ALA A 168 SHEET 7 A 7 PHE A 320 ALA A 321 1 O ALA A 321 N PHE A 285 SHEET 1 B 2 ILE A 176 THR A 177 0 SHEET 2 B 2 ARG A 192 ILE A 193 -1 O ARG A 192 N THR A 177 SHEET 1 C 5 TYR A 390 ASN A 394 0 SHEET 2 C 5 ARG A 417 ASP A 421 1 O ARG A 417 N VAL A 391 SHEET 3 C 5 VAL A 366 VAL A 370 1 N VAL A 367 O ILE A 420 SHEET 4 C 5 CYS A 444 PHE A 449 1 O PHE A 449 N VAL A 370 SHEET 5 C 5 GLU A 496 ILE A 500 1 O LEU A 498 N CYS A 446 LINK C GLN A 218 N MSE A 219 1555 1555 1.33 LINK C MSE A 219 N GLY A 220 1555 1555 1.33 LINK C GLY A 263 N MSE A 264 1555 1555 1.33 LINK C MSE A 264 N TRP A 265 1555 1555 1.33 LINK C GLU A 464 N MSE A 465 1555 1555 1.33 LINK C MSE A 465 N THR A 466 1555 1555 1.33 LINK C ASP A 475 N MSE A 476 1555 1555 1.33 LINK C MSE A 476 N VAL A 477 1555 1555 1.33 LINK C VAL A 477 N MSE A 478 1555 1555 1.33 LINK C MSE A 478 N PHE A 479 1555 1555 1.33 LINK O1 PO4 X 523 MG MG A 529 1555 1555 1.96 LINK O ASP A 172 MG MG A 529 1555 1555 2.24 LINK OD1 ASP A 288 MG MG A 529 1555 1555 2.27 LINK OD2 ASP A 288 MG MG A 529 1555 1555 2.99 LINK MG MG A 529 O HOH A 5 1555 1555 2.07 LINK MG MG A 529 O HOH A 20 1555 1555 2.08 LINK O3' DA X 402 P PO4 X 523 1555 1555 1.61 CISPEP 1 LYS A 259 PRO A 260 0 7.16 CISPEP 2 LEU A 353 PRO A 354 0 -0.83 SITE 1 AC1 10 HOH A 5 ALA A 170 LEU A 171 ASP A 172 SITE 2 AC1 10 THR A 216 ASN A 217 LYS A 259 MG A 529 SITE 3 AC1 10 HOH X 66 DA X 402 SITE 1 AC2 9 HOH A 70 PRO A 338 PHE A 340 PRO A 342 SITE 2 AC2 9 HIS A 458 ARG A 461 PHE A 519 SER A 520 SITE 3 AC2 9 GLU A 521 SITE 1 AC3 6 HOH A 29 VAL A 160 LYS A 161 GLN A 163 SITE 2 AC3 6 TYR A 210 PRO A 245 SITE 1 AC4 5 HOH A 125 LYS A 201 LEU A 205 GLU A 208 SITE 2 AC4 5 TYR A 210 SITE 1 AC5 9 HOH A 49 HOH A 51 PHE A 372 GLY A 374 SITE 2 AC5 9 ALA A 375 GLY A 376 LYS A 377 SER A 378 SITE 3 AC5 9 HOH A 588 SITE 1 AC6 5 HOH A 5 HOH A 20 ASP A 172 ASP A 288 SITE 2 AC6 5 PO4 X 523 CRYST1 77.160 43.030 127.270 90.00 107.12 90.00 C 1 2 1 4 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 0.012960 0.000000 0.003992 0.00000 SCALE2 0.000000 0.023240 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008222 0.00000