10 20 30 40 50 60 70 80 3U7F - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE,TRANSFERASE/DNA 13-OCT-11 3U7F
TITLE CRYSTAL STRUCTURE OF MPNKP CATALYTIC FRAGMENT (D170A) BOUND TO SINGLE- TITLE 2 STRANDED DNA (TCCTCP)
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; 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 2 29-AUG-12 3U7F 1 JRNL REVDAT 1 14-DEC-11 3U7F 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. 1.80 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : -3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 33002 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1649 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.47 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 47.37 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.50440 REMARK 3 B22 (A**2) : -0.40910 REMARK 3 B33 (A**2) : -0.82660 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : -0.97230 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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): 2.1475 -16.3123 48.7576 REMARK 3 T TENSOR REMARK 3 T11: -0.0240 T22: -0.0287 REMARK 3 T33: -0.0562 T12: 0.0252 REMARK 3 T13: 0.0220 T23: -0.0386 REMARK 3 L TENSOR REMARK 3 L11: 0.0258 L22: 0.0112 REMARK 3 L33: 0.0289 L12: 0.0005 REMARK 3 L13: -0.0103 L23: 0.0064 REMARK 3 S TENSOR REMARK 3 S11: -0.0270 S12: -0.0292 S13: -0.0185 REMARK 3 S21: 0.0180 S22: -0.0294 S23: -0.0184 REMARK 3 S31: 0.0318 S32: 0.0115 S33: -0.1901 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: chain B and (resseq 218:242) REMARK 3 ORIGIN FOR THE GROUP (A): 9.3418 -24.5141 47.3882 REMARK 3 T TENSOR REMARK 3 T11: 0.0460 T22: -0.0222 REMARK 3 T33: -0.0059 T12: 0.0421 REMARK 3 T13: 0.0241 T23: 0.0816 REMARK 3 L TENSOR REMARK 3 L11: 0.0454 L22: 0.0654 REMARK 3 L33: 0.0239 L12: -0.0400 REMARK 3 L13: 0.0165 L23: -0.0199 REMARK 3 S TENSOR REMARK 3 S11: 0.0079 S12: 0.0185 S13: -0.0016 REMARK 3 S21: -0.0189 S22: -0.0185 S23: -0.0356 REMARK 3 S31: 0.0163 S32: 0.0300 S33: -0.0176 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: chain B and (resseq 243:316) REMARK 3 ORIGIN FOR THE GROUP (A): 4.7981 -11.1701 38.9089 REMARK 3 T TENSOR REMARK 3 T11: -0.1016 T22: -0.1132 REMARK 3 T33: -0.0133 T12: -0.0963 REMARK 3 T13: 0.0071 T23: 0.0254 REMARK 3 L TENSOR REMARK 3 L11: 0.0159 L22: 0.0282 REMARK 3 L33: 0.0383 L12: -0.0077 REMARK 3 L13: -0.0111 L23: -0.0276 REMARK 3 S TENSOR REMARK 3 S11: -0.0277 S12: -0.0169 S13: 0.0274 REMARK 3 S21: 0.0166 S22: -0.0000 S23: -0.0271 REMARK 3 S31: -0.0071 S32: 0.0192 S33: -0.0776 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: chain B and (resseq 317:341) REMARK 3 ORIGIN FOR THE GROUP (A): 7.5256 -0.2026 42.1020 REMARK 3 T TENSOR REMARK 3 T11: 0.0363 T22: -0.0382 REMARK 3 T33: 0.0436 T12: -0.0246 REMARK 3 T13: 0.0067 T23: -0.0306 REMARK 3 L TENSOR REMARK 3 L11: 0.0241 L22: 0.0454 REMARK 3 L33: 0.1041 L12: -0.0074 REMARK 3 L13: 0.0058 L23: -0.0018 REMARK 3 S TENSOR REMARK 3 S11: 0.0039 S12: -0.0064 S13: 0.0395 REMARK 3 S21: 0.0066 S22: -0.0009 S23: -0.0585 REMARK 3 S31: -0.0598 S32: 0.0254 S33: -0.0320 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: chain B and (resseq 342:384) REMARK 3 ORIGIN FOR THE GROUP (A): 20.6106 -8.1825 5.8845 REMARK 3 T TENSOR REMARK 3 T11: -0.0010 T22: 0.0461 REMARK 3 T33: -0.0016 T12: 0.0557 REMARK 3 T13: 0.0225 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.0650 L22: 0.1394 REMARK 3 L33: 0.1966 L12: 0.0736 REMARK 3 L13: 0.0402 L23: -0.0471 REMARK 3 S TENSOR REMARK 3 S11: 0.0023 S12: 0.0016 S13: 0.0124 REMARK 3 S21: 0.0193 S22: 0.0020 S23: 0.0372 REMARK 3 S31: -0.0317 S32: -0.0739 S33: -0.0230 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: chain B and (resseq 385:466) REMARK 3 ORIGIN FOR THE GROUP (A): 30.1872 -14.7943 7.3278 REMARK 3 T TENSOR REMARK 3 T11: 0.0478 T22: 0.0476 REMARK 3 T33: -0.0116 T12: 0.0285 REMARK 3 T13: 0.0048 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 0.2258 L22: 0.2277 REMARK 3 L33: 0.3412 L12: 0.1441 REMARK 3 L13: 0.1046 L23: -0.0090 REMARK 3 S TENSOR REMARK 3 S11: -0.0057 S12: 0.0689 S13: -0.0544 REMARK 3 S21: -0.0774 S22: -0.0014 S23: -0.0568 REMARK 3 S31: 0.0891 S32: 0.1372 S33: -0.0058 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: chain B and (resseq 467:484) REMARK 3 ORIGIN FOR THE GROUP (A): 26.5302 -15.4238 23.1480 REMARK 3 T TENSOR REMARK 3 T11: 0.0640 T22: 0.1606 REMARK 3 T33: 0.0739 T12: 0.0314 REMARK 3 T13: -0.0440 T23: -0.0309 REMARK 3 L TENSOR REMARK 3 L11: 0.0094 L22: 0.0147 REMARK 3 L33: 0.0092 L12: -0.0119 REMARK 3 L13: -0.0093 L23: 0.0119 REMARK 3 S TENSOR REMARK 3 S11: 0.0070 S12: -0.0249 S13: -0.0266 REMARK 3 S21: 0.0410 S22: -0.0097 S23: -0.0278 REMARK 3 S31: 0.0036 S32: 0.0304 S33: -0.0061 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: chain B and (resseq 485:522) REMARK 3 ORIGIN FOR THE GROUP (A): 18.4788 -6.9288 14.1216 REMARK 3 T TENSOR REMARK 3 T11: 0.0057 T22: 0.0258 REMARK 3 T33: 0.0104 T12: -0.0150 REMARK 3 T13: -0.0286 T23: 0.0206 REMARK 3 L TENSOR REMARK 3 L11: 0.1585 L22: 0.1675 REMARK 3 L33: 0.0319 L12: 0.0480 REMARK 3 L13: 0.0105 L23: 0.0183 REMARK 3 S TENSOR REMARK 3 S11: -0.0166 S12: 0.0523 S13: 0.0321 REMARK 3 S21: -0.0786 S22: 0.0315 S23: -0.0013 REMARK 3 S31: -0.0177 S32: 0.0044 S33: 0.0120 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 3U7F 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 RCSB ID CODE IS RCSB068400.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-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 : 33004 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 46.000 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) : 0.12700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.62000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.630 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 (%): 40.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 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 31.16500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL 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 GLU B 506 REMARK 465 HIS B 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 LYS B 150 CG CD CE NZ REMARK 470 ARG B 395 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 402 CG CD OE1 NE2 REMARK 470 ARG B 432 CD NE CZ NH1 NH2 REMARK 470 GLN B 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 HD1 HIS B 458 HO1 GOL B 529 1.15 REMARK 500 O HOH B 695 O HOH B 703 1.96 REMARK 500 O HOH B 717 O HOH B 720 1.96 REMARK 500 O HOH B 537 O HOH B 709 1.99 REMARK 500 O HOH B 685 O HOH B 721 2.00 REMARK 500 O HOH B 66 O HOH B 574 2.02 REMARK 500 O HOH B 64 O HOH B 638 2.04 REMARK 500 O HOH B 64 O HOH B 762 2.06 REMARK 500 O HOH B 109 O HOH B 592 2.08 REMARK 500 O HOH B 663 O HOH B 744 2.12 REMARK 500 O HOH B 686 O HOH B 699 2.12 REMARK 500 O HOH B 33 O HOH B 788 2.13 REMARK 500 O HOH B 592 O HOH B 737 2.15 REMARK 500 O HOH B 94 O HOH B 793 2.15 REMARK 500 OE2 GLU B 355 O HOH B 707 2.15 REMARK 500 O HOH B 772 O HOH B 773 2.16 REMARK 500 O HOH B 694 O HOH B 790 2.17 REMARK 500 O HOH B 611 O HOH B 650 2.18 REMARK 500 O HOH B 777 O HOH B 795 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 699 O HOH B 707 2645 1.97 REMARK 500 O HOH B 582 O HOH B 650 1655 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT X 401 P DT X 401 O5' -0.079 REMARK 500 REMARK 500 REMARK: NULL 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 X 402 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU B 171 -72.05 -104.04 REMARK 500 THR B 174 -57.25 -121.97 REMARK 500 ARG B 300 57.46 -115.72 REMARK 500 ALA B 348 -156.52 -61.97 REMARK 500 REMARK 500 REMARK: NULL
REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PO4 X 523
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 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 288 OD1 REMARK 620 2 ASP B 172 O 80.7 REMARK 620 3 ASP B 288 OD2 52.3 92.7 REMARK 620 4 HOH B 759 O 110.1 78.0 63.1 REMARK 620 5 HOH B 653 O 113.9 155.6 111.7 112.1 REMARK 620 6 PO4 X 523 O1 133.6 78.5 167.1 105.5 77.5 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 MG B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 529 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 530 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 531 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 532 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 533
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: 3U7G RELATED DB: PDB REMARK 900 RELATED ID: 3U7H RELATED DB: PDB
DBREF 3U7F B 142 522 UNP Q9JLV6 PNKP_MOUSE 142 522 DBREF 3U7F X 398 402 PDB 3U7F 3U7F 398 402
SEQADV 3U7F 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 DC
MODRES 3U7F MSE B 219 MET SELENOMETHIONINE MODRES 3U7F MSE B 264 MET SELENOMETHIONINE MODRES 3U7F CSO B 450 CYS S-HYDROXYCYSTEINE MODRES 3U7F MSE B 465 MET SELENOMETHIONINE MODRES 3U7F MSE B 476 MET SELENOMETHIONINE MODRES 3U7F 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 31 HET MSE B 478 17 HET PO4 X 523 4 HET MG B 1 1 HET GOL B 529 14 HET GOL B 530 14 HET GOL B 531 14 HET GOL B 532 14 HET PO4 B 533 5
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 3 PO4 2(O4 P 3-) FORMUL 4 MG MG 2+ FORMUL 5 GOL 4(C3 H8 O3) FORMUL 10 HOH *409(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 SER B 279 SER B 283 5 5 HELIX 6 6 CYS B 307 GLY B 317 1 11 HELIX 7 7 THR B 322 LYS B 329 1 8 HELIX 8 8 ASP B 341 ILE B 345 5 5 HELIX 9 9 GLY B 376 LEU B 385 1 10 HELIX 10 10 VAL B 386 GLY B 389 5 4 HELIX 11 11 ASN B 394 GLY B 399 1 6 HELIX 12 12 SER B 400 GLN B 414 1 15 HELIX 13 13 ASP B 426 GLY B 441 1 16 HELIX 14 14 THR B 452 ASP B 467 1 16 HELIX 15 15 SER B 474 PHE B 485 1 12 HELIX 16 16 THR B 489 GLY B 493 5 5 HELIX 17 17 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 250 N LEU B 153 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 1.32 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 OD1 ASP B 288 MG MG B 1 1555 1555 2.16 LINK O ASP B 172 MG MG B 1 1555 1555 2.33 LINK OD2 ASP B 288 MG MG B 1 1555 1555 2.69 LINK MG MG B 1 O HOH B 759 1555 1555 2.03 LINK MG MG B 1 O HOH B 653 1555 1555 2.04 LINK O1 PO4 X 523 MG MG B 1 1555 1555 2.16 LINK O3' DC X 402 P PO4 X 523 1555 1555 1.61
CISPEP 1 LYS B 259 PRO B 260 0 12.45 CISPEP 2 LEU B 353 PRO B 354 0 -3.89
SITE 1 AC1 10 MG B 1 ALA B 170 LEU B 171 ASP B 172 SITE 2 AC1 10 THR B 216 ASN B 217 LYS B 259 HOH B 651 SITE 3 AC1 10 HOH B 653 DC X 402 SITE 1 AC2 5 ASP B 172 ASP B 288 HOH B 653 HOH B 759 SITE 2 AC2 5 PO4 X 523 SITE 1 AC3 8 HOH B 71 PRO B 338 PHE B 340 HIS B 458 SITE 2 AC3 8 ARG B 461 PHE B 519 SER B 520 GLU B 521 SITE 1 AC4 9 HOH B 10 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 589 SITE 1 AC5 7 HOH B 40 HOH B 61 ARG B 310 PHE B 320 SITE 2 AC5 7 GLU B 325 PHE B 335 HOH B 643 SITE 1 AC6 5 LYS B 201 LEU B 205 TYR B 210 VAL B 284 SITE 2 AC6 5 HOH B 767 SITE 1 AC7 11 HOH B 34 PHE B 372 PRO B 373 GLY B 374 SITE 2 AC7 11 ALA B 375 GLY B 376 LYS B 377 SER B 378 SITE 3 AC7 11 ARG B 463 HOH B 577 HOH B 710
CRYST1 42.600 62.330 67.970 90.00 91.81 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 0.023474 0.000000 0.000742 0.00000
SCALE2 0.000000 0.016044 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014720 0.00000