HEADER TRANSFERASE/DNA BINDING PROTEIN 14-JAN-05 1YJM TITLE CRYSTAL STRUCTURE OF THE FHA DOMAIN OF MOUSE POLYNUCLEOTIDE KINASE IN TITLE 2 COMPLEX WITH AN XRCC4-DERIVED PHOSPHOPEPTIDE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYNUCLEOTIDE 5'-HYDROXYL-KINASE; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: FHA DOMAIN; COMPND 5 EC: 2.7.1.78; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 12-MER PEPTIDE FROM DNA-REPAIR PROTEIN XRCC4; COMPND 9 CHAIN: E, F, G; COMPND 10 SYNONYM: X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 4; COMPND 11 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 GENE: PNK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD 99; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST15; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: CHEMICALLY SYNTHESIZED PHOSPHO-PEPTIDE KEYWDS POLYNUCLEOTIDE KINASE, FHA DOMAIN, XRCC4 PHOSPHOPEPTIDE, TRANSFERASE- KEYWDS 2 DNA BINDING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.K.BERNSTEIN,R.S.WILLIAMS,M.L.RAKOVSZKY,D.CUI,R.GREEN,F.KARIMI- AUTHOR 2 BUSHERI,R.S.MANI,S.GALICIA,C.A.KOCH,C.E.CASS,D.DUROCHER,M.WEINFELD, AUTHOR 3 J.N.M.GLOVER REVDAT 5 16-OCT-24 1YJM 1 REMARK REVDAT 4 25-OCT-23 1YJM 1 REMARK LINK REVDAT 3 13-JUL-11 1YJM 1 VERSN REVDAT 2 24-FEB-09 1YJM 1 VERSN REVDAT 1 15-MAR-05 1YJM 0 JRNL AUTH N.K.BERNSTEIN,R.S.WILLIAMS,M.L.RAKOVSZKY,D.CUI,R.GREEN, JRNL AUTH 2 F.KARIMI-BUSHERI,R.S.MANI,S.GALICIA,C.A.KOCH,C.E.CASS, JRNL AUTH 3 D.DUROCHER,M.WEINFELD,J.N.GLOVER JRNL TITL THE MOLECULAR ARCHITECTURE OF THE MAMMALIAN DNA REPAIR JRNL TITL 2 ENZYME, POLYNUCLEOTIDE KINASE. JRNL REF MOL.CELL V. 17 657 2005 JRNL REFN ISSN 1097-2765 JRNL PMID 15749016 JRNL DOI 10.1016/J.MOLCEL.2005.02.012 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.5 REMARK 3 NUMBER OF REFLECTIONS : 18994 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1022 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1085 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2531 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 188 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21000 REMARK 3 B22 (A**2) : -0.74000 REMARK 3 B33 (A**2) : 0.53000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.284 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.213 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.142 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.338 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2582 ; 0.005 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2407 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3526 ; 0.862 ; 2.022 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5603 ; 0.669 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 326 ; 5.026 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;37.548 ;23.960 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 407 ;10.997 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;10.402 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 403 ; 0.055 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2823 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 463 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 349 ; 0.163 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2311 ; 0.149 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1169 ; 0.157 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1586 ; 0.070 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 168 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 9 ; 0.167 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 33 ; 0.101 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.077 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2124 ; 0.192 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 679 ; 0.022 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2667 ; 0.208 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1052 ; 0.282 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 859 ; 0.430 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 110 REMARK 3 ORIGIN FOR THE GROUP (A): 17.3060 11.3340 58.9500 REMARK 3 T TENSOR REMARK 3 T11: -0.0768 T22: -0.0514 REMARK 3 T33: -0.0409 T12: -0.0003 REMARK 3 T13: 0.0074 T23: 0.0198 REMARK 3 L TENSOR REMARK 3 L11: 1.3170 L22: 1.4649 REMARK 3 L33: 1.7753 L12: 0.1501 REMARK 3 L13: 0.0054 L23: -0.2676 REMARK 3 S TENSOR REMARK 3 S11: -0.0265 S12: -0.0734 S13: -0.0232 REMARK 3 S21: 0.0350 S22: 0.0559 S23: 0.0057 REMARK 3 S31: -0.0739 S32: 0.0262 S33: -0.0295 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 6 B 110 REMARK 3 ORIGIN FOR THE GROUP (A): 29.7800 24.8750 47.4170 REMARK 3 T TENSOR REMARK 3 T11: -0.0665 T22: -0.0595 REMARK 3 T33: -0.0343 T12: -0.0258 REMARK 3 T13: -0.0135 T23: 0.0125 REMARK 3 L TENSOR REMARK 3 L11: 1.1524 L22: 1.3144 REMARK 3 L33: 1.7687 L12: 0.1699 REMARK 3 L13: 0.0218 L23: -0.0188 REMARK 3 S TENSOR REMARK 3 S11: 0.0403 S12: 0.0151 S13: 0.0453 REMARK 3 S21: 0.0510 S22: -0.1182 S23: -0.0500 REMARK 3 S31: -0.0999 S32: -0.0121 S33: 0.0779 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 7 C 107 REMARK 3 ORIGIN FOR THE GROUP (A): 11.0730 13.1910 82.4580 REMARK 3 T TENSOR REMARK 3 T11: -0.0469 T22: -0.0947 REMARK 3 T33: -0.0493 T12: 0.0288 REMARK 3 T13: 0.0081 T23: -0.0127 REMARK 3 L TENSOR REMARK 3 L11: 2.0791 L22: 2.3950 REMARK 3 L33: 2.0227 L12: -0.2964 REMARK 3 L13: -0.0566 L23: 0.1610 REMARK 3 S TENSOR REMARK 3 S11: 0.0647 S12: -0.0035 S13: -0.0942 REMARK 3 S21: -0.0664 S22: -0.0072 S23: 0.0086 REMARK 3 S31: -0.0791 S32: -0.0104 S33: -0.0574 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 3 E 10 REMARK 3 ORIGIN FOR THE GROUP (A): 0.2230 10.1720 51.1870 REMARK 3 T TENSOR REMARK 3 T11: -0.1590 T22: 0.0286 REMARK 3 T33: -0.0527 T12: 0.0342 REMARK 3 T13: -0.0555 T23: 0.0950 REMARK 3 L TENSOR REMARK 3 L11: 5.8014 L22: 6.1495 REMARK 3 L33: 4.1740 L12: 2.3135 REMARK 3 L13: 2.6225 L23: -2.9065 REMARK 3 S TENSOR REMARK 3 S11: -0.0747 S12: 0.3277 S13: 0.1373 REMARK 3 S21: 0.1242 S22: -0.1334 S23: 0.1874 REMARK 3 S31: 0.3668 S32: -0.6540 S33: 0.2081 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 3 F 10 REMARK 3 ORIGIN FOR THE GROUP (A): 47.0220 17.8330 45.5830 REMARK 3 T TENSOR REMARK 3 T11: -0.1655 T22: -0.0297 REMARK 3 T33: 0.0295 T12: 0.0561 REMARK 3 T13: -0.0145 T23: 0.1047 REMARK 3 L TENSOR REMARK 3 L11: 6.2493 L22: 4.3058 REMARK 3 L33: 5.5404 L12: 1.9905 REMARK 3 L13: 1.0934 L23: -0.6191 REMARK 3 S TENSOR REMARK 3 S11: -0.0248 S12: 0.3077 S13: -0.1632 REMARK 3 S21: -0.1480 S22: -0.0486 S23: -0.7473 REMARK 3 S31: 0.2146 S32: 0.3864 S33: 0.0734 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : G 3 G 8 REMARK 3 ORIGIN FOR THE GROUP (A): 1.2590 3.7480 70.9170 REMARK 3 T TENSOR REMARK 3 T11: 0.0541 T22: 0.1802 REMARK 3 T33: 0.0563 T12: 0.0481 REMARK 3 T13: -0.0970 T23: -0.0185 REMARK 3 L TENSOR REMARK 3 L11: 5.4265 L22: 8.7572 REMARK 3 L33: 2.5179 L12: 6.8936 REMARK 3 L13: 3.6964 L23: 4.6957 REMARK 3 S TENSOR REMARK 3 S11: -1.1859 S12: -0.0104 S13: -0.2821 REMARK 3 S21: -1.4501 S22: 0.3537 S23: -0.0861 REMARK 3 S31: 1.3998 S32: -1.6981 S33: 0.8322 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1YJM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031587. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1159 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18994 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05100 REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.19400 REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: THE FHA DOMAIN FROM THE FULL-LENGTH MOUSE PNK REMARK 200 STRUCTURE, 1YJ5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA CITRATE (PH 5.5), 25% PEG REMARK 280 4000, 0.2M LI2SO4, 5MM DTT, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 68.35500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.35500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 25.57750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.49950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.57750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.49950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.35500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.57750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.49950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 68.35500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.57750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 61.49950 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 300 REMARK: THE BIOLOGICAL UNIT IS A MONOMER OF FULL-LENGTH REMARK 300 POLYNUCLEOTIDE KINASE. 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: 1220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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 350 REMARK 350 BIOMOLECULE: 2 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: 1130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F 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 350 REMARK 350 BIOMOLECULE: 3 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: 1040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, G 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 119 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 SER A 2 REMARK 465 GLN A 3 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 GLN B 3 REMARK 465 LEU B 4 REMARK 465 GLY B 5 REMARK 465 MET C 1 REMARK 465 SER C 2 REMARK 465 GLN C 3 REMARK 465 LEU C 4 REMARK 465 GLY C 5 REMARK 465 SER C 6 REMARK 465 GLU C 108 REMARK 465 LEU C 109 REMARK 465 SER C 110 REMARK 465 GLU E 11 REMARK 465 SER E 12 REMARK 465 GLU E 13 REMARK 465 LYS E 14 REMARK 465 LYS E 15 REMARK 465 GLU F 11 REMARK 465 SER F 12 REMARK 465 GLU F 13 REMARK 465 LYS F 14 REMARK 465 LYS F 15 REMARK 465 ASP G 9 REMARK 465 GLU G 10 REMARK 465 GLU G 11 REMARK 465 SER G 12 REMARK 465 GLU G 13 REMARK 465 LYS G 14 REMARK 465 LYS G 15 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 4 CB CG CD1 CD2 REMARK 470 SER A 6 OG REMARK 470 SER A 110 OG REMARK 470 SER B 6 OG REMARK 470 SER B 110 OG REMARK 470 ARG C 7 CB CG CD NE CZ NH1 NH2 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 TYR A 100 68.79 61.83 REMARK 500 ASN B 49 76.62 -118.56 REMARK 500 TYR B 100 70.45 64.78 REMARK 500 ASN C 49 76.22 -110.60 REMARK 500 TYR C 100 69.33 66.67 REMARK 500 ASP G 5 38.68 -152.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACE E 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACE F 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACE G 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YJ5 RELATED DB: PDB REMARK 900 MOUSE POLYNUCLEOTIDE KINASE DBREF 1YJM A 1 110 UNP Q9JLV6 PNKP_MOUSE 1 110 DBREF 1YJM B 1 110 UNP Q9JLV6 PNKP_MOUSE 1 110 DBREF 1YJM C 1 110 UNP Q9JLV6 PNKP_MOUSE 1 110 DBREF 1YJM E 3 15 PDB 1YJM 1YJM 3 15 DBREF 1YJM F 3 15 PDB 1YJM 1YJM 3 15 DBREF 1YJM G 3 15 PDB 1YJM 1YJM 3 15 SEQRES 1 A 110 MET SER GLN LEU GLY SER ARG GLY ARG LEU TRP LEU GLN SEQRES 2 A 110 SER PRO THR GLY GLY PRO PRO PRO ILE PHE LEU PRO SER SEQRES 3 A 110 ASP GLY GLN ALA LEU VAL LEU GLY ARG GLY PRO LEU THR SEQRES 4 A 110 GLN VAL THR ASP ARG LYS CYS SER ARG ASN GLN VAL GLU SEQRES 5 A 110 LEU ILE ALA ASP PRO GLU SER ARG THR VAL ALA VAL LYS SEQRES 6 A 110 GLN LEU GLY VAL ASN PRO SER THR VAL GLY VAL HIS GLU SEQRES 7 A 110 LEU LYS PRO GLY LEU SER GLY SER LEU SER LEU GLY ASP SEQRES 8 A 110 VAL LEU TYR LEU VAL ASN GLY LEU TYR PRO LEU THR LEU SEQRES 9 A 110 ARG TRP GLU GLU LEU SER SEQRES 1 B 110 MET SER GLN LEU GLY SER ARG GLY ARG LEU TRP LEU GLN SEQRES 2 B 110 SER PRO THR GLY GLY PRO PRO PRO ILE PHE LEU PRO SER SEQRES 3 B 110 ASP GLY GLN ALA LEU VAL LEU GLY ARG GLY PRO LEU THR SEQRES 4 B 110 GLN VAL THR ASP ARG LYS CYS SER ARG ASN GLN VAL GLU SEQRES 5 B 110 LEU ILE ALA ASP PRO GLU SER ARG THR VAL ALA VAL LYS SEQRES 6 B 110 GLN LEU GLY VAL ASN PRO SER THR VAL GLY VAL HIS GLU SEQRES 7 B 110 LEU LYS PRO GLY LEU SER GLY SER LEU SER LEU GLY ASP SEQRES 8 B 110 VAL LEU TYR LEU VAL ASN GLY LEU TYR PRO LEU THR LEU SEQRES 9 B 110 ARG TRP GLU GLU LEU SER SEQRES 1 C 110 MET SER GLN LEU GLY SER ARG GLY ARG LEU TRP LEU GLN SEQRES 2 C 110 SER PRO THR GLY GLY PRO PRO PRO ILE PHE LEU PRO SER SEQRES 3 C 110 ASP GLY GLN ALA LEU VAL LEU GLY ARG GLY PRO LEU THR SEQRES 4 C 110 GLN VAL THR ASP ARG LYS CYS SER ARG ASN GLN VAL GLU SEQRES 5 C 110 LEU ILE ALA ASP PRO GLU SER ARG THR VAL ALA VAL LYS SEQRES 6 C 110 GLN LEU GLY VAL ASN PRO SER THR VAL GLY VAL HIS GLU SEQRES 7 C 110 LEU LYS PRO GLY LEU SER GLY SER LEU SER LEU GLY ASP SEQRES 8 C 110 VAL LEU TYR LEU VAL ASN GLY LEU TYR PRO LEU THR LEU SEQRES 9 C 110 ARG TRP GLU GLU LEU SER SEQRES 1 E 13 ACE TYR ASP GLU SER TPO ASP GLU GLU SER GLU LYS LYS SEQRES 1 F 13 ACE TYR ASP GLU SER TPO ASP GLU GLU SER GLU LYS LYS SEQRES 1 G 13 ACE TYR ASP GLU SER TPO ASP GLU GLU SER GLU LYS LYS MODRES 1YJM TPO E 8 THR PHOSPHOTHREONINE MODRES 1YJM TPO F 8 THR PHOSPHOTHREONINE MODRES 1YJM TPO G 8 THR PHOSPHOTHREONINE HET ACE E 3 3 HET TPO E 8 11 HET ACE F 3 3 HET TPO F 8 11 HET ACE G 3 3 HET TPO G 8 11 HETNAM ACE ACETYL GROUP HETNAM TPO PHOSPHOTHREONINE HETSYN TPO PHOSPHONOTHREONINE FORMUL 4 ACE 3(C2 H4 O) FORMUL 4 TPO 3(C4 H10 N O6 P) FORMUL 7 HOH *188(H2 O) SHEET 1 A 6 ILE A 22 PHE A 23 0 SHEET 2 A 6 GLY A 8 GLN A 13 -1 N LEU A 12 O ILE A 22 SHEET 3 A 6 LEU A 99 GLU A 108 -1 O THR A 103 N GLN A 13 SHEET 4 A 6 VAL A 92 VAL A 96 -1 N LEU A 93 O LEU A 102 SHEET 5 A 6 THR A 73 VAL A 74 -1 N THR A 73 O TYR A 94 SHEET 6 A 6 HIS A 77 GLU A 78 -1 O HIS A 77 N VAL A 74 SHEET 1 B 4 LEU A 31 LEU A 33 0 SHEET 2 B 4 VAL A 51 ASP A 56 -1 O VAL A 51 N LEU A 33 SHEET 3 B 4 THR A 61 GLN A 66 -1 O LYS A 65 N GLU A 52 SHEET 4 B 4 SER A 84 SER A 88 -1 O GLY A 85 N VAL A 64 SHEET 1 C 6 ILE B 22 PHE B 23 0 SHEET 2 C 6 GLY B 8 GLN B 13 -1 N LEU B 12 O ILE B 22 SHEET 3 C 6 LEU B 99 GLU B 108 -1 O ARG B 105 N TRP B 11 SHEET 4 C 6 VAL B 92 VAL B 96 -1 N LEU B 93 O LEU B 102 SHEET 5 C 6 THR B 73 VAL B 74 -1 N THR B 73 O TYR B 94 SHEET 6 C 6 HIS B 77 GLU B 78 -1 O HIS B 77 N VAL B 74 SHEET 1 D 4 LEU B 31 LEU B 33 0 SHEET 2 D 4 VAL B 51 ASP B 56 -1 O LEU B 53 N LEU B 31 SHEET 3 D 4 THR B 61 GLN B 66 -1 O ALA B 63 N ILE B 54 SHEET 4 D 4 SER B 84 LEU B 87 -1 O GLY B 85 N VAL B 64 SHEET 1 E 6 ILE C 22 PHE C 23 0 SHEET 2 E 6 ARG C 9 GLN C 13 -1 N LEU C 12 O ILE C 22 SHEET 3 E 6 LEU C 99 GLU C 107 -1 O GLU C 107 N ARG C 9 SHEET 4 E 6 VAL C 92 VAL C 96 -1 N LEU C 93 O LEU C 102 SHEET 5 E 6 THR C 73 VAL C 74 -1 N THR C 73 O TYR C 94 SHEET 6 E 6 HIS C 77 GLU C 78 -1 O HIS C 77 N VAL C 74 SHEET 1 F 4 LEU C 31 LEU C 33 0 SHEET 2 F 4 VAL C 51 ASP C 56 -1 O LEU C 53 N LEU C 31 SHEET 3 F 4 THR C 61 GLN C 66 -1 O THR C 61 N ASP C 56 SHEET 4 F 4 SER C 84 LEU C 87 -1 O GLY C 85 N VAL C 64 LINK C ACE E 3 N TYR E 4 1555 1555 1.33 LINK C SER E 7 N TPO E 8 1555 1555 1.33 LINK C TPO E 8 N ASP E 9 1555 1555 1.33 LINK C ACE F 3 N TYR F 4 1555 1555 1.33 LINK C SER F 7 N TPO F 8 1555 1555 1.33 LINK C TPO F 8 N ASP F 9 1555 1555 1.33 LINK C ACE G 3 N TYR G 4 1555 1555 1.33 LINK C SER G 7 N TPO G 8 1555 1555 1.33 CISPEP 1 ASP F 9 GLU F 10 0 7.36 SITE 1 AC1 1 HOH A 157 SITE 1 AC2 4 ARG B 35 ASP F 5 HOH B 155 HOH F 134 SITE 1 AC3 1 ASP G 5 CRYST1 51.155 122.999 136.710 90.00 90.00 90.00 C 2 2 21 24 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 0.019548 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008130 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007315 0.00000