HEADER HYDROLASE 15-MAY-01 1IPI TITLE CRYSTAL STRUCTURE OF THE ARCHAEAL HOLLIDAY JUNCTION RESOLVASE HJC FROM TITLE 2 PYROCOCCUS FURIOSUS FORM II COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOLLIDAY JUNCTION RESOLVASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HJC; COMPND 5 EC: 3.1.22.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 GENE: HJC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS NUCLEASE FOLD, HJC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.NISHINO,K.KOMORI,Y.ISHINO,K.MORIKAWA REVDAT 4 25-OCT-23 1IPI 1 REMARK REVDAT 3 24-FEB-09 1IPI 1 VERSN REVDAT 2 14-JAN-03 1IPI 1 REMARK REVDAT 1 28-NOV-01 1IPI 0 JRNL AUTH T.NISHINO,K.KOMORI,Y.ISHINO,K.MORIKAWA JRNL TITL DISSECTION OF THE REGIONAL ROLES OF THE ARCHAEAL HOLLIDAY JRNL TITL 2 JUNCTION RESOLVASE HJC BY STRUCTURAL AND MUTATIONAL JRNL TITL 3 ANALYSES. JRNL REF J.BIOL.CHEM. V. 276 35735 2001 JRNL REFN ISSN 0021-9258 JRNL PMID 11441015 JRNL DOI 10.1074/JBC.M104460200 REMARK 2 REMARK 2 RESOLUTION. 2.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11621 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 SET) : 0.214 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 11.480 REMARK 3 FREE R VALUE TEST SET COUNT : 1334 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.24 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 0.78 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 120 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1802 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 157 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.19 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.84 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.618 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IPI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAY-01. REMARK 100 THE DEPOSITION ID IS D_1000005150. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL24XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.834 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13043 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 41.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.27900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1GEF FUNCTIONAL DIMER REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS-HCL, 1MM EDTA, 32.5% REMARK 280 PEG4000, 10% GLYCEROL , PH 7.0, VAPOR DIFFUSION, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 89.70267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.85133 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 67.27700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.42567 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 112.12833 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 300 REMARK: CHAIN A AND B FORM FUNCTIONAL DIMER 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: 1960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ILE A 115 REMARK 465 GLN A 116 REMARK 465 LYS A 117 REMARK 465 THR A 118 REMARK 465 LEU A 119 REMARK 465 GLU A 120 REMARK 465 GLY A 121 REMARK 465 LYS A 122 REMARK 465 SER A 123 REMARK 465 ILE B 115 REMARK 465 GLN B 116 REMARK 465 LYS B 117 REMARK 465 THR B 118 REMARK 465 LEU B 119 REMARK 465 GLU B 120 REMARK 465 GLY B 121 REMARK 465 LYS B 122 REMARK 465 SER B 123 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 LYS A 31 -110.85 -106.34 REMARK 500 LYS A 40 -19.52 -144.82 REMARK 500 VAL A 85 -32.40 -158.24 REMARK 500 LEU A 113 -84.44 -92.23 REMARK 500 TYR B 2 101.45 91.91 REMARK 500 LYS B 31 -117.29 -109.31 REMARK 500 LEU B 83 56.33 -60.52 REMARK 500 ASN B 84 -46.29 -175.09 REMARK 500 LEU B 112 6.68 -62.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GEF RELATED DB: PDB REMARK 900 1GEF IS CRYSTALLIZED WITH AMMONIUM SULFATE. DBREF 1IPI A 1 123 UNP Q9V301 Q9V301_PYRFU 1 123 DBREF 1IPI B 1 123 UNP Q9V301 Q9V301_PYRFU 1 123 SEQRES 1 A 123 MET TYR ARG LYS GLY ALA GLN ALA GLU ARG GLU LEU ILE SEQRES 2 A 123 LYS LEU LEU GLU LYS HIS GLY PHE ALA VAL VAL ARG SER SEQRES 3 A 123 ALA GLY SER LYS LYS VAL ASP LEU VAL ALA GLY ASN GLY SEQRES 4 A 123 LYS LYS TYR LEU CYS ILE GLU VAL LYS VAL THR LYS LYS SEQRES 5 A 123 ASP HIS LEU TYR VAL GLY LYS ARG ASP MET GLY ARG LEU SEQRES 6 A 123 ILE GLU PHE SER ARG ARG PHE GLY GLY ILE PRO VAL LEU SEQRES 7 A 123 ALA VAL LYS PHE LEU ASN VAL GLY TRP ARG PHE ILE GLU SEQRES 8 A 123 VAL SER PRO LYS ILE GLU LYS PHE VAL PHE THR PRO SER SEQRES 9 A 123 SER GLY VAL SER LEU GLU VAL LEU LEU GLY ILE GLN LYS SEQRES 10 A 123 THR LEU GLU GLY LYS SER SEQRES 1 B 123 MET TYR ARG LYS GLY ALA GLN ALA GLU ARG GLU LEU ILE SEQRES 2 B 123 LYS LEU LEU GLU LYS HIS GLY PHE ALA VAL VAL ARG SER SEQRES 3 B 123 ALA GLY SER LYS LYS VAL ASP LEU VAL ALA GLY ASN GLY SEQRES 4 B 123 LYS LYS TYR LEU CYS ILE GLU VAL LYS VAL THR LYS LYS SEQRES 5 B 123 ASP HIS LEU TYR VAL GLY LYS ARG ASP MET GLY ARG LEU SEQRES 6 B 123 ILE GLU PHE SER ARG ARG PHE GLY GLY ILE PRO VAL LEU SEQRES 7 B 123 ALA VAL LYS PHE LEU ASN VAL GLY TRP ARG PHE ILE GLU SEQRES 8 B 123 VAL SER PRO LYS ILE GLU LYS PHE VAL PHE THR PRO SER SEQRES 9 B 123 SER GLY VAL SER LEU GLU VAL LEU LEU GLY ILE GLN LYS SEQRES 10 B 123 THR LEU GLU GLY LYS SER FORMUL 3 HOH *157(H2 O) HELIX 1 1 GLY A 5 HIS A 19 1 15 HELIX 2 2 GLY A 58 GLY A 73 1 16 HELIX 3 3 SER A 108 GLY A 114 1 7 HELIX 4 4 GLY B 5 HIS B 19 1 15 HELIX 5 5 GLY B 58 GLY B 73 1 16 HELIX 6 6 THR B 102 GLY B 106 5 5 HELIX 7 7 GLU B 110 GLY B 114 5 5 SHEET 1 A 5 ALA A 22 ARG A 25 0 SHEET 2 A 5 LEU A 34 GLY A 37 -1 O VAL A 35 N VAL A 24 SHEET 3 A 5 TYR A 42 THR A 50 -1 O LEU A 43 N ALA A 36 SHEET 4 A 5 ILE A 75 PHE A 82 1 N ILE A 75 O TYR A 42 SHEET 5 A 5 GLY A 86 GLU A 91 -1 N GLY A 86 O PHE A 82 SHEET 1 B 2 LEU A 55 VAL A 57 0 SHEET 2 B 2 PHE A 99 PHE A 101 -1 O PHE A 99 N VAL A 57 SHEET 1 C 5 ALA B 22 ARG B 25 0 SHEET 2 C 5 LEU B 34 GLY B 37 -1 O VAL B 35 N VAL B 24 SHEET 3 C 5 TYR B 42 THR B 50 -1 O LEU B 43 N ALA B 36 SHEET 4 C 5 ILE B 75 PHE B 82 1 N ILE B 75 O TYR B 42 SHEET 5 C 5 GLY B 86 GLU B 91 -1 N GLY B 86 O PHE B 82 SHEET 1 D 2 LEU B 55 VAL B 57 0 SHEET 2 D 2 PHE B 99 PHE B 101 -1 O PHE B 99 N VAL B 57 CRYST1 59.969 59.969 134.554 90.00 90.00 120.00 P 65 12 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 0.016675 0.009627 0.000000 0.00000 SCALE2 0.000000 0.019255 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007432 0.00000