HEADER HYDROLASE/TRANSFERASE/DNA 25-JUL-11 3ZVN TITLE THE STRUCTURAL BASIS FOR SUBSTRATE RECOGNITION BY MAMMALIAN TITLE 2 POLYNUCLEOTIDE KINASE 3' PHOSPHATASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: POLYNUCLEOTIDE 3'-PHOSPHATASE AND POLYNUCLEOTIDE 5'- COMPND 5 HYDROXYL-KINASE DOMAINS, RESIDUES 111-522; COMPND 6 SYNONYM: DNA 5'-KINASE/3'-PHOSPHATASE, POLYNUCLEOTIDE KINASE-3'- COMPND 7 PHOSPHATASE, PNKP; 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: 5'-D(*GP*TP*CP*AP*CP)-3'; COMPND 13 CHAIN: E, F, G, H, I; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PTWO-E; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE-TRANSFERASE-DNA COMPLEX, BASE EXCISION REPAIR, BER, NON- KEYWDS 2 HOMOLOGOUS END-JOINING, NHEJ, DNA REPAIR, CANCER EXPDTA X-RAY DIFFRACTION AUTHOR F.GARCES,L.H.PEARL,A.W.OLIVER REVDAT 3 20-DEC-23 3ZVN 1 REMARK LINK REVDAT 2 07-MAR-18 3ZVN 1 SOURCE JRNL REVDAT 1 16-NOV-11 3ZVN 0 JRNL AUTH F.GARCES,L.H.PEARL,A.W.OLIVER JRNL TITL THE STRUCTURAL BASIS FOR SUBSTRATE RECOGNITION BY MAMMALIAN JRNL TITL 2 POLYNUCLEOTIDE KINASE 3' PHOSPHATASE. JRNL REF MOL. CELL V. 44 385 2011 JRNL REFN ISSN 1097-4164 JRNL PMID 22055185 JRNL DOI 10.1016/J.MOLCEL.2011.08.036 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.2 REMARK 3 NUMBER OF REFLECTIONS : 28753 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1484 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 36.5002 - 4.7783 0.79 2340 139 0.2110 0.2437 REMARK 3 2 4.7783 - 3.7940 0.86 2438 136 0.1718 0.2375 REMARK 3 3 3.7940 - 3.3147 0.88 2466 139 0.1816 0.2851 REMARK 3 4 3.3147 - 3.0118 0.90 2493 126 0.1868 0.2809 REMARK 3 5 3.0118 - 2.7960 0.90 2491 137 0.2108 0.2582 REMARK 3 6 2.7960 - 2.6312 0.91 2508 133 0.2165 0.2955 REMARK 3 7 2.6312 - 2.4995 0.91 2504 138 0.2266 0.3018 REMARK 3 8 2.4995 - 2.3907 0.92 2509 129 0.2293 0.3040 REMARK 3 9 2.3907 - 2.2987 0.92 2509 133 0.2360 0.2731 REMARK 3 10 2.2987 - 2.2194 0.92 2528 133 0.2610 0.2781 REMARK 3 11 2.2194 - 2.1500 0.92 2483 141 0.2944 0.3298 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 : 0.72 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 62.44 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.530 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -11.51960 REMARK 3 B22 (A**2) : -12.25940 REMARK 3 B33 (A**2) : 23.77900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.007 3565 REMARK 3 ANGLE : 1.298 4945 REMARK 3 CHIRALITY : 0.069 536 REMARK 3 PLANARITY : 0.004 562 REMARK 3 DIHEDRAL : 19.598 1336 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3ZVN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1290049161. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28753 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 36.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.2 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.66000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS TRIS PH 5.5, 0.1 M AMMONIUM REMARK 280 ACETATE, 17 % (W/V) PEG 10000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 34.63500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.22000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.49500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.22000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.63500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.49500 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E, F, G, H, I 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASP 170 TO ASN 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 A 107 REMARK 465 PRO A 108 REMARK 465 HIS A 109 REMARK 465 MET A 110 REMARK 465 THR A 111 REMARK 465 SER A 112 REMARK 465 GLY A 113 REMARK 465 SER A 114 REMARK 465 GLN A 115 REMARK 465 PRO A 116 REMARK 465 ASP A 117 REMARK 465 ALA A 118 REMARK 465 PRO A 119 REMARK 465 PRO A 120 REMARK 465 ASP A 121 REMARK 465 THR A 122 REMARK 465 PRO A 123 REMARK 465 GLY A 124 REMARK 465 ASP A 125 REMARK 465 PRO A 126 REMARK 465 GLU A 127 REMARK 465 GLU A 128 REMARK 465 GLY A 129 REMARK 465 GLU A 130 REMARK 465 ASP A 131 REMARK 465 THR A 132 REMARK 465 GLU A 133 REMARK 465 PRO A 134 REMARK 465 GLN A 135 REMARK 465 LYS A 136 REMARK 465 LYS A 137 REMARK 465 ARG A 138 REMARK 465 VAL A 139 REMARK 465 ARG A 140 REMARK 465 LYS A 141 REMARK 465 SER A 142 REMARK 465 SER A 143 REMARK 465 LEU A 144 REMARK 465 GLY A 145 REMARK 465 DC E 5 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 LEU A 149 CG CD1 CD2 REMARK 470 LYS A 150 CG CD CE NZ REMARK 470 LYS A 151 CD CE NZ REMARK 470 SER A 158 OG REMARK 470 LYS A 161 CG CD CE NZ REMARK 470 LEU A 226 CG CD1 CD2 REMARK 470 GLU A 229 CG CD OE1 OE2 REMARK 470 LEU A 268 CG CD1 CD2 REMARK 470 LYS A 301 CG CD CE NZ REMARK 470 LYS A 302 CG CD CE NZ REMARK 470 ARG A 334 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 499 CD OE1 OE2 REMARK 470 GLN A 513 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 O3' DT I 2 O HOH I 2003 2.02 REMARK 500 N1 DA E 4 O HOH E 2002 2.04 REMARK 500 OG SER A 180 OD2 ASP A 190 2.06 REMARK 500 O4 DT I 2 O HOH E 2005 2.16 REMARK 500 N4 DC H 3 O HOH F 2002 2.17 REMARK 500 OG SER A 387 O HOH A 2108 2.17 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 DG E 1 C4 DG E 1 C5 0.076 REMARK 500 DG E 1 C5 DG E 1 C6 0.060 REMARK 500 DG E 1 C6 DG E 1 N1 -0.047 REMARK 500 DG E 1 C5 DG E 1 N7 -0.041 REMARK 500 DG E 1 N7 DG E 1 C8 0.046 REMARK 500 DG E 1 N9 DG E 1 C4 -0.051 REMARK 500 DG F 1 C4 DG F 1 C5 0.086 REMARK 500 DG F 1 C5 DG F 1 C6 0.064 REMARK 500 DG F 1 C6 DG F 1 N1 -0.050 REMARK 500 DG F 1 C5 DG F 1 N7 -0.038 REMARK 500 DG F 1 N7 DG F 1 C8 0.061 REMARK 500 DG G 1 C4 DG G 1 C5 0.088 REMARK 500 DG G 1 C6 DG G 1 N1 -0.049 REMARK 500 DG G 1 C5 DG G 1 N7 -0.039 REMARK 500 DG G 1 N7 DG G 1 C8 0.056 REMARK 500 DG H 1 C4 DG H 1 C5 0.087 REMARK 500 DG H 1 C5 DG H 1 C6 0.062 REMARK 500 DG H 1 C6 DG H 1 N1 -0.052 REMARK 500 DG H 1 C5 DG H 1 N7 -0.044 REMARK 500 DG H 1 N7 DG H 1 C8 0.055 REMARK 500 DG I 1 C4 DG I 1 C5 0.090 REMARK 500 DG I 1 C6 DG I 1 N1 -0.050 REMARK 500 DG I 1 C5 DG I 1 N7 -0.040 REMARK 500 DG I 1 N7 DG I 1 C8 0.052 REMARK 500 DG I 1 N9 DG I 1 C4 -0.051 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 DG E 1 C2 - N3 - C4 ANGL. DEV. = 8.5 DEGREES REMARK 500 DG E 1 N3 - C4 - C5 ANGL. DEV. = -8.4 DEGREES REMARK 500 DG E 1 C5 - C6 - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 DG E 1 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG E 1 C5 - N7 - C8 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG E 1 C8 - N9 - C4 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG E 1 N3 - C4 - N9 ANGL. DEV. = 7.9 DEGREES REMARK 500 DG E 1 C6 - C5 - N7 ANGL. DEV. = 6.2 DEGREES REMARK 500 DG E 1 C5 - C6 - O6 ANGL. DEV. = -8.5 DEGREES REMARK 500 DC E 3 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 DG F 1 C2 - N3 - C4 ANGL. DEV. = 8.8 DEGREES REMARK 500 DG F 1 N3 - C4 - C5 ANGL. DEV. = -9.1 DEGREES REMARK 500 DG F 1 C5 - C6 - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 DG F 1 C4 - C5 - N7 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG F 1 N3 - C4 - N9 ANGL. DEV. = 7.5 DEGREES REMARK 500 DG F 1 C6 - C5 - N7 ANGL. DEV. = 6.5 DEGREES REMARK 500 DG F 1 C5 - C6 - O6 ANGL. DEV. = -6.6 DEGREES REMARK 500 DC F 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG G 1 C2 - N3 - C4 ANGL. DEV. = 8.7 DEGREES REMARK 500 DG G 1 N3 - C4 - C5 ANGL. DEV. = -9.2 DEGREES REMARK 500 DG G 1 C5 - C6 - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 DG G 1 C4 - C5 - N7 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG G 1 C5 - N7 - C8 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG G 1 C8 - N9 - C4 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG G 1 N3 - C4 - N9 ANGL. DEV. = 8.5 DEGREES REMARK 500 DG G 1 C6 - C5 - N7 ANGL. DEV. = 5.8 DEGREES REMARK 500 DG G 1 C5 - C6 - O6 ANGL. DEV. = -7.7 DEGREES REMARK 500 DC G 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG H 1 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG H 1 C2 - N3 - C4 ANGL. DEV. = 8.7 DEGREES REMARK 500 DG H 1 N3 - C4 - C5 ANGL. DEV. = -9.6 DEGREES REMARK 500 DG H 1 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 DG H 1 C4 - C5 - N7 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG H 1 C5 - N7 - C8 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG H 1 N3 - C4 - N9 ANGL. DEV. = 8.2 DEGREES REMARK 500 DG H 1 C6 - C5 - N7 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG H 1 C5 - C6 - O6 ANGL. DEV. = -7.3 DEGREES REMARK 500 DC H 3 O4' - C1' - N1 ANGL. DEV. = -5.6 DEGREES REMARK 500 DC H 5 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DG I 1 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG I 1 C2 - N3 - C4 ANGL. DEV. = 8.1 DEGREES REMARK 500 DG I 1 N3 - C4 - C5 ANGL. DEV. = -8.3 DEGREES REMARK 500 DG I 1 C5 - C6 - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 DG I 1 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG I 1 C5 - N7 - C8 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG I 1 C8 - N9 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG I 1 N3 - C4 - N9 ANGL. DEV. = 8.0 DEGREES REMARK 500 DG I 1 C6 - C5 - N7 ANGL. DEV. = 6.4 DEGREES REMARK 500 DG I 1 C5 - C6 - O6 ANGL. DEV. = -7.6 DEGREES REMARK 500 DC I 3 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 51 ANGLE DEVIATIONS. 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 149 -166.27 -105.09 REMARK 500 LEU A 171 -81.50 -84.54 REMARK 500 THR A 174 -52.32 -123.55 REMARK 500 GLU A 274 43.69 -90.63 REMARK 500 PRO A 277 159.80 -47.15 REMARK 500 ASN A 424 61.34 37.03 REMARK 500 GLU A 506 -73.62 -53.25 REMARK 500 HIS A 507 34.03 -91.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2023 DISTANCE = 5.99 ANGSTROMS 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 MN A 901 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 378 OG REMARK 620 2 ADP A1524 O1B 91.5 REMARK 620 3 HOH A2104 O 84.2 173.7 REMARK 620 4 HOH A2105 O 88.6 84.6 90.8 REMARK 620 5 HOH A2106 O 88.4 94.1 90.3 176.7 REMARK 620 6 HOH A2208 O 174.8 91.1 92.9 87.2 95.9 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 MN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1523 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 1524 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1525 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZVL RELATED DB: PDB REMARK 900 THE STRUCTURAL BASIS FOR SUBSTRATE RECOGNITION BY MAMMALIAN REMARK 900 POLYNUCLEOTIDE KINASE 3' PHOSPHATASE REMARK 900 RELATED ID: 1UJX RELATED DB: PDB REMARK 900 THE FORKHEAD ASSOCIATED (FHA) DOMAIN LIKE STRUCTURE FROMMOUSE REMARK 900 POLYNUCLEOTIDE KINASE 3'-PHOSPHATASE REMARK 900 RELATED ID: 1YJ5 RELATED DB: PDB REMARK 900 MOLECULAR ARCHITECTURE OF MAMMALIAN POLYNUCLEOTIDE KINASE, A DNA REMARK 900 REPAIR ENZYME REMARK 900 RELATED ID: 1YJM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE FHA DOMAIN OF MOUSE POLYNUCLEOTIDEKINASE REMARK 900 IN COMPLEX WITH AN XRCC4-DERIVED PHOSPHOPEPTIDE. REMARK 900 RELATED ID: 3ZVM RELATED DB: PDB REMARK 900 THE STRUCTURAL BASIS FOR SUBSTRATE RECOGNITION BY MAMMALIAN REMARK 900 POLYNUCLEOTIDE KINASE 3' PHOSPHATASE DBREF 3ZVN A 111 522 UNP Q9JLV6 PNKP_MOUSE 111 522 DBREF 3ZVN E 1 5 PDB 3ZVN 3ZVN 1 5 DBREF 3ZVN F 1 5 PDB 3ZVN 3ZVN 1 5 DBREF 3ZVN G 1 5 PDB 3ZVN 3ZVN 1 5 DBREF 3ZVN H 1 5 PDB 3ZVN 3ZVN 1 5 DBREF 3ZVN I 1 5 PDB 3ZVN 3ZVN 1 5 SEQADV 3ZVN GLY A 107 UNP Q9JLV6 EXPRESSION TAG SEQADV 3ZVN PRO A 108 UNP Q9JLV6 EXPRESSION TAG SEQADV 3ZVN HIS A 109 UNP Q9JLV6 EXPRESSION TAG SEQADV 3ZVN MET A 110 UNP Q9JLV6 EXPRESSION TAG SEQADV 3ZVN ASN A 170 UNP Q9JLV6 ASP 170 ENGINEERED MUTATION SEQRES 1 A 416 GLY PRO HIS MET THR SER GLY SER GLN PRO ASP ALA PRO SEQRES 2 A 416 PRO ASP THR PRO GLY ASP PRO GLU GLU GLY GLU ASP THR SEQRES 3 A 416 GLU PRO GLN LYS LYS ARG VAL ARG LYS SER SER LEU GLY SEQRES 4 A 416 TRP GLU SER LEU LYS LYS LEU LEU VAL PHE THR ALA SER SEQRES 5 A 416 GLY VAL LYS PRO GLN GLY LYS VAL ALA ALA PHE ASN LEU SEQRES 6 A 416 ASP GLY THR LEU ILE THR THR ARG SER GLY LYS VAL PHE SEQRES 7 A 416 PRO THR SER PRO SER ASP TRP ARG ILE LEU TYR PRO GLU SEQRES 8 A 416 ILE PRO LYS LYS LEU GLN GLU LEU ALA ALA GLU GLY TYR SEQRES 9 A 416 LYS LEU VAL ILE PHE THR ASN GLN MET GLY ILE GLY ARG SEQRES 10 A 416 GLY LYS LEU PRO ALA GLU VAL PHE LYS GLY LYS VAL GLU SEQRES 11 A 416 ALA VAL LEU GLU LYS LEU GLY VAL PRO PHE GLN VAL LEU SEQRES 12 A 416 VAL ALA THR HIS ALA GLY LEU ASN ARG LYS PRO VAL SER SEQRES 13 A 416 GLY MET TRP ASP HIS LEU GLN GLU GLN ALA ASN GLU GLY SEQRES 14 A 416 ILE PRO ILE SER VAL GLU ASP SER VAL PHE VAL GLY ASP SEQRES 15 A 416 ALA ALA GLY ARG LEU ALA ASN TRP ALA PRO GLY ARG LYS SEQRES 16 A 416 LYS LYS ASP PHE SER CYS ALA ASP ARG LEU PHE ALA LEU SEQRES 17 A 416 ASN VAL GLY LEU PRO PHE ALA THR PRO GLU GLU PHE PHE SEQRES 18 A 416 LEU LYS TRP PRO ALA ALA ARG PHE GLU LEU PRO ALA PHE SEQRES 19 A 416 ASP PRO ARG THR ILE SER SER ALA GLY PRO LEU TYR LEU SEQRES 20 A 416 PRO GLU SER SER SER LEU LEU SER PRO ASN PRO GLU VAL SEQRES 21 A 416 VAL VAL ALA VAL GLY PHE PRO GLY ALA GLY LYS SER THR SEQRES 22 A 416 PHE ILE GLN GLU HIS LEU VAL SER ALA GLY TYR VAL HIS SEQRES 23 A 416 VAL ASN ARG ASP THR LEU GLY SER TRP GLN ARG CYS VAL SEQRES 24 A 416 SER SER CYS GLN ALA ALA LEU ARG GLN GLY LYS ARG VAL SEQRES 25 A 416 VAL ILE ASP ASN THR ASN PRO ASP VAL PRO SER ARG ALA SEQRES 26 A 416 ARG TYR ILE GLN CYS ALA LYS ASP ALA GLY VAL PRO CYS SEQRES 27 A 416 ARG CYS PHE ASN PHE CSX ALA THR ILE GLU GLN ALA ARG SEQRES 28 A 416 HIS ASN ASN ARG PHE ARG GLU MET THR ASP PRO SER HIS SEQRES 29 A 416 ALA PRO VAL SER ASP MET VAL MET PHE SER TYR ARG LYS SEQRES 30 A 416 GLN PHE GLU PRO PRO THR LEU ALA GLU GLY PHE LEU GLU SEQRES 31 A 416 ILE LEU GLU ILE PRO PHE ARG LEU GLN GLU HIS LEU ASP SEQRES 32 A 416 PRO ALA LEU GLN ARG LEU TYR ARG GLN PHE SER GLU GLY SEQRES 1 E 5 DG DT DC DA DC SEQRES 1 F 5 DG DT DC DA DC SEQRES 1 G 5 DG DT DC DA DC SEQRES 1 H 5 DG DT DC DA DC SEQRES 1 I 5 DG DT DC DA DC MODRES 3ZVN CSX A 450 CYS S-OXY CYSTEINE HET CSX A 450 7 HET MN A 901 1 HET GOL A1523 6 HET ADP A1524 27 HET GOL A1525 6 HETNAM CSX S-OXY CYSTEINE HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 CSX C3 H7 N O3 S FORMUL 7 MN MN 2+ FORMUL 8 GOL 2(C3 H8 O3) FORMUL 9 ADP C10 H15 N5 O10 P2 FORMUL 11 HOH *253(H2 O) HELIX 1 1 PRO A 196 GLU A 208 1 13 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 LEU A 328 1 7 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 GLY A 389 5 4 HELIX 10 10 ASN A 394 GLY A 399 1 6 HELIX 11 11 SER A 400 GLN A 414 1 15 HELIX 12 12 ASP A 426 GLY A 441 1 16 HELIX 13 13 THR A 452 ASP A 467 1 16 HELIX 14 14 SER A 474 PHE A 485 1 12 HELIX 15 15 THR A 489 GLY A 493 5 5 HELIX 16 16 ASP A 509 GLN A 518 1 10 SHEET 1 AA 7 SER A 148 LEU A 149 0 SHEET 2 AA 7 LEU A 152 THR A 156 -1 O LEU A 152 N LEU A 149 SHEET 3 AA 7 GLN A 247 ALA A 251 -1 O VAL A 248 N PHE A 155 SHEET 4 AA 7 LYS A 211 ASN A 217 1 O LEU A 212 N GLN A 247 SHEET 5 AA 7 VAL A 166 PHE A 169 1 O ALA A 167 N VAL A 213 SHEET 6 AA 7 VAL A 284 VAL A 286 1 O VAL A 284 N ALA A 168 SHEET 7 AA 7 PHE A 320 ALA A 321 1 N ALA A 321 O PHE A 285 SHEET 1 AB 2 ILE A 176 THR A 177 0 SHEET 2 AB 2 ARG A 192 ILE A 193 -1 O ARG A 192 N THR A 177 SHEET 1 AC 5 VAL A 391 VAL A 393 0 SHEET 2 AC 5 VAL A 418 ILE A 420 1 O VAL A 419 N VAL A 393 SHEET 3 AC 5 VAL A 366 VAL A 370 1 O VAL A 367 N ILE A 420 SHEET 4 AC 5 CYS A 444 PHE A 449 1 O ARG A 445 N VAL A 368 SHEET 5 AC 5 GLU A 496 ILE A 500 1 O GLU A 496 N CYS A 446 LINK C PHE A 449 N CSX A 450 1555 1555 1.33 LINK C CSX A 450 N ALA A 451 1555 1555 1.33 LINK OG SER A 378 MN MN A 901 1555 1555 2.22 LINK MN MN A 901 O1B ADP A1524 1555 1555 2.15 LINK MN MN A 901 O HOH A2104 1555 1555 2.33 LINK MN MN A 901 O HOH A2105 1555 1555 2.46 LINK MN MN A 901 O HOH A2106 1555 1555 2.38 LINK MN MN A 901 O HOH A2208 1555 1555 2.31 CISPEP 1 LYS A 259 PRO A 260 0 8.60 CISPEP 2 LEU A 353 PRO A 354 0 -3.34 SITE 1 AC1 6 SER A 378 ADP A1524 HOH A2104 HOH A2105 SITE 2 AC1 6 HOH A2106 HOH A2208 SITE 1 AC2 10 ALA A 375 GLY A 376 PHE A 380 PHE A 449 SITE 2 AC2 10 PRO A 501 PHE A 502 ARG A 503 ADP A1524 SITE 3 AC2 10 HOH A2101 HOH A2209 SITE 1 AC3 20 PHE A 372 GLY A 374 ALA A 375 GLY A 376 SITE 2 AC3 20 LYS A 377 SER A 378 THR A 379 ASN A 459 SITE 3 AC3 20 PHE A 462 ARG A 463 PHE A 502 ARG A 503 SITE 4 AC3 20 LEU A 504 GLN A 505 MN A 901 GOL A1523 SITE 5 AC3 20 HOH A2105 HOH A2178 HOH A2208 HOH A2210 SITE 1 AC4 1 HOH A2064 CRYST1 69.270 72.990 114.440 90.00 90.00 90.00 P 21 21 21 20 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 0.014436 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013701 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008738 0.00000