HEADER HYDROLASE 17-APR-12 4EP4 TITLE THERMUS THERMOPHILUS RUVC STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HOLLIDAY JUNCTION NUCLEASE RUVC, HOLLIDAY JUNCTION RESOLVASE COMPND 5 RUVC; COMPND 6 EC: 3.1.22.4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 GENE: RUVC, TTHA1090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RESOLVASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.CHEN,K.SHI,Z.Q.YIN,H.AIHARA REVDAT 4 28-FEB-24 4EP4 1 REMARK REVDAT 3 03-DEC-14 4EP4 1 AUTHOR REVDAT 2 16-JAN-13 4EP4 1 JRNL REVDAT 1 14-NOV-12 4EP4 0 JRNL AUTH L.CHEN,K.SHI,Z.YIN,H.AIHARA JRNL TITL STRUCTURAL ASYMMETRY IN THE THERMUS THERMOPHILUS RUVC DIMER JRNL TITL 2 SUGGESTS A BASIS FOR SEQUENTIAL STRAND CLEAVAGES DURING JRNL TITL 3 HOLLIDAY JUNCTION RESOLUTION. JRNL REF NUCLEIC ACIDS RES. V. 41 648 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23118486 JRNL DOI 10.1093/NAR/GKS1015 REMARK 2 REMARK 2 RESOLUTION. 1.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 1.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 65393 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 35.4959 - 3.0820 0.98 4827 153 0.1630 0.1739 REMARK 3 2 3.0820 - 2.4464 1.00 4710 148 0.1595 0.2426 REMARK 3 3 2.4464 - 2.1372 1.00 4663 147 0.1437 0.1595 REMARK 3 4 2.1372 - 1.9418 1.00 4647 146 0.1393 0.1579 REMARK 3 5 1.9418 - 1.8027 1.00 4631 147 0.1367 0.1758 REMARK 3 6 1.8027 - 1.6964 1.00 4590 145 0.1299 0.1853 REMARK 3 7 1.6964 - 1.6114 1.00 4594 144 0.1293 0.1701 REMARK 3 8 1.6114 - 1.5413 1.00 4564 144 0.1285 0.1848 REMARK 3 9 1.5413 - 1.4819 0.99 4556 144 0.1416 0.2015 REMARK 3 10 1.4819 - 1.4308 0.96 4338 137 0.1595 0.2082 REMARK 3 11 1.4308 - 1.3861 0.96 4404 139 0.1823 0.2438 REMARK 3 12 1.3861 - 1.3464 0.96 4384 138 0.1814 0.2405 REMARK 3 13 1.3464 - 1.3110 0.97 4361 138 0.2053 0.2538 REMARK 3 14 1.3110 - 1.2790 0.90 4124 130 0.1978 0.2393 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 45.89 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.69960 REMARK 3 B22 (A**2) : 4.68820 REMARK 3 B33 (A**2) : -3.98870 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 : 0.005 2692 REMARK 3 ANGLE : 1.008 3665 REMARK 3 CHIRALITY : 0.064 411 REMARK 3 PLANARITY : 0.005 477 REMARK 3 DIHEDRAL : 14.694 1001 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 4EP4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071896. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 96 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65468 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.280 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : 0.04800 REMARK 200 FOR THE DATA SET : 28.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.42300 REMARK 200 R SYM FOR SHELL (I) : 0.42300 REMARK 200 FOR SHELL : 2.130 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG400, LI2SO4, AND SODIUM ACETATE, PH REMARK 280 4.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 18.38850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.45500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.57550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.45500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.38850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.57550 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 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 PRO A 8 -127.27 -70.84 REMARK 500 REMARK 500 REMARK: NULL 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 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 7 OD2 REMARK 620 2 HOH B 328 O 93.7 REMARK 620 3 HOH B 448 O 76.3 162.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EP5 RELATED DB: PDB DBREF 4EP4 A 1 166 UNP Q5SJC4 RUVC_THET8 1 166 DBREF 4EP4 B 1 166 UNP Q5SJC4 RUVC_THET8 1 166 SEQRES 1 A 166 MET VAL VAL ALA GLY ILE ASP PRO GLY ILE THR HIS LEU SEQRES 2 A 166 GLY LEU GLY VAL VAL ALA VAL GLU GLY LYS GLY ALA LEU SEQRES 3 A 166 LYS ALA ARG LEU LEU HIS GLY GLU VAL VAL LYS THR SER SEQRES 4 A 166 PRO GLN GLU PRO ALA LYS GLU ARG VAL GLY ARG ILE HIS SEQRES 5 A 166 ALA ARG VAL LEU GLU VAL LEU HIS ARG PHE ARG PRO GLU SEQRES 6 A 166 ALA VAL ALA VAL GLU GLU GLN PHE PHE TYR ARG GLN ASN SEQRES 7 A 166 GLU LEU ALA TYR LYS VAL GLY TRP ALA LEU GLY ALA VAL SEQRES 8 A 166 LEU VAL ALA ALA PHE GLU ALA GLY VAL PRO VAL TYR ALA SEQRES 9 A 166 TYR GLY PRO MET GLN VAL LYS GLN ALA LEU ALA GLY HIS SEQRES 10 A 166 GLY HIS ALA ALA LYS GLU GLU VAL ALA LEU MET VAL ARG SEQRES 11 A 166 GLY ILE LEU GLY LEU LYS GLU ALA PRO ARG PRO SER HIS SEQRES 12 A 166 LEU ALA ASP ALA LEU ALA ILE ALA LEU THR HIS ALA PHE SEQRES 13 A 166 TYR ALA ARG MET GLY THR ALA LYS PRO LEU SEQRES 1 B 166 MET VAL VAL ALA GLY ILE ASP PRO GLY ILE THR HIS LEU SEQRES 2 B 166 GLY LEU GLY VAL VAL ALA VAL GLU GLY LYS GLY ALA LEU SEQRES 3 B 166 LYS ALA ARG LEU LEU HIS GLY GLU VAL VAL LYS THR SER SEQRES 4 B 166 PRO GLN GLU PRO ALA LYS GLU ARG VAL GLY ARG ILE HIS SEQRES 5 B 166 ALA ARG VAL LEU GLU VAL LEU HIS ARG PHE ARG PRO GLU SEQRES 6 B 166 ALA VAL ALA VAL GLU GLU GLN PHE PHE TYR ARG GLN ASN SEQRES 7 B 166 GLU LEU ALA TYR LYS VAL GLY TRP ALA LEU GLY ALA VAL SEQRES 8 B 166 LEU VAL ALA ALA PHE GLU ALA GLY VAL PRO VAL TYR ALA SEQRES 9 B 166 TYR GLY PRO MET GLN VAL LYS GLN ALA LEU ALA GLY HIS SEQRES 10 B 166 GLY HIS ALA ALA LYS GLU GLU VAL ALA LEU MET VAL ARG SEQRES 11 B 166 GLY ILE LEU GLY LEU LYS GLU ALA PRO ARG PRO SER HIS SEQRES 12 B 166 LEU ALA ASP ALA LEU ALA ILE ALA LEU THR HIS ALA PHE SEQRES 13 B 166 TYR ALA ARG MET GLY THR ALA LYS PRO LEU HET MG B 201 1 HET GOL B 202 6 HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MG MG 2+ FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *411(H2 O) HELIX 1 1 PRO A 43 ARG A 63 1 21 HELIX 2 2 ASN A 78 GLY A 99 1 22 HELIX 3 3 GLY A 106 GLY A 116 1 11 HELIX 4 4 ALA A 121 LEU A 133 1 13 HELIX 5 5 PRO A 141 MET A 160 1 20 HELIX 6 6 PRO B 43 ARG B 63 1 21 HELIX 7 7 LEU B 80 GLY B 99 1 20 HELIX 8 8 GLY B 106 GLY B 116 1 11 HELIX 9 9 ALA B 121 LEU B 133 1 13 HELIX 10 10 PRO B 141 GLY B 161 1 21 SHEET 1 A 5 ALA A 28 LYS A 37 0 SHEET 2 A 5 HIS A 12 VAL A 20 -1 N LEU A 13 O VAL A 36 SHEET 3 A 5 VAL A 2 ASP A 7 -1 N GLY A 5 O GLY A 16 SHEET 4 A 5 ALA A 66 GLU A 70 1 O ALA A 68 N ALA A 4 SHEET 5 A 5 VAL A 102 TYR A 105 1 O TYR A 103 N VAL A 67 SHEET 1 B 5 ALA B 28 LYS B 37 0 SHEET 2 B 5 HIS B 12 VAL B 20 -1 N VAL B 17 O LEU B 31 SHEET 3 B 5 VAL B 2 ASP B 7 -1 N GLY B 5 O GLY B 16 SHEET 4 B 5 ALA B 66 GLU B 70 1 O ALA B 68 N ALA B 4 SHEET 5 B 5 VAL B 102 TYR B 105 1 O TYR B 103 N VAL B 67 LINK OD2 ASP B 7 MG MG B 201 1555 1555 2.09 LINK MG MG B 201 O HOH B 328 1555 1555 2.22 LINK MG MG B 201 O HOH B 448 1555 1555 2.40 CISPEP 1 ARG A 140 PRO A 141 0 -3.22 CISPEP 2 ARG B 140 PRO B 141 0 -1.31 SITE 1 AC1 4 ASP B 7 HIS B 143 HOH B 328 HOH B 448 SITE 1 AC2 9 GLU A 123 HOH A 341 MET B 1 GLU B 65 SITE 2 AC2 9 ALA B 158 HOH B 307 HOH B 319 HOH B 402 SITE 3 AC2 9 HOH B 439 CRYST1 36.777 51.151 134.910 90.00 90.00 90.00 P 21 21 21 8 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 0.027191 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019550 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007412 0.00000