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 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,VAGIN,DODSON 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1052 ; 0.282 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 859 ; 0.430 ; 4.500 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 RCSB ID CODE IS RCSB031587. 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 ACE F 3 N TYR F 4 1555 1555 1.33 LINK C ACE G 3 N TYR G 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 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 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 MASTER 487 0 6 0 30 0 3 6 0 0 0 30 END