HEADER LIGASE 25-MAR-04 1VDX TITLE CRYSTAL STRUCTURE OF A PYROCOCCUS HORIKOSHII PROTEIN WITH SIMILARITIES TITLE 2 TO 2'5' RNA-LIGASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN PH0099; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 2'-5' RNA LIGASE RELATED PROTEIN; COMPND 5 EC: 6.5.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-11A KEYWDS LIGASE, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 2 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA X-RAY DIFFRACTION AUTHOR P.H.REHSE,T.H.TAHIROV,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE AUTHOR 2 (RSGI) REVDAT 4 25-OCT-23 1VDX 1 REMARK REVDAT 3 24-FEB-09 1VDX 1 VERSN REVDAT 2 14-FEB-06 1VDX 1 JRNL REMARK REVDAT 1 12-APR-05 1VDX 0 JRNL AUTH P.H.REHSE,T.H.TAHIROV JRNL TITL STRUCTURE OF A PUTATIVE 2'-5' RNA LIGASE FROM PYROCOCCUS JRNL TITL 2 HORIKOSHII. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 61 1207 2005 JRNL REFN ISSN 0907-4449 JRNL PMID 16131753 JRNL DOI 10.1107/S0907444905017841 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 399182.780 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 7386 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) : 0.225 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.500 REMARK 3 FREE R VALUE TEST SET COUNT : 552 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1045 REMARK 3 BIN R VALUE (WORKING SET) : 0.2770 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 83 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1488 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.96000 REMARK 3 B22 (A**2) : -2.81000 REMARK 3 B33 (A**2) : -3.16000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.27 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) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.31 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.910 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.290 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.800 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.240 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.130 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 40.31 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VDX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000006507. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-SEP-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7670 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.410 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.33 REMARK 200 R MERGE FOR SHELL (I) : 0.42300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.360 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1IUH.PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES, PEG 4000, PH 5.8, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 22.03400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.58550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.73550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.58550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.03400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.73550 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 LYS A 44 121.07 -177.19 REMARK 500 ASN A 96 104.51 61.81 REMARK 500 PHE A 133 145.05 -178.51 REMARK 500 PRO A 169 -75.93 -19.45 REMARK 500 SER A 183 -168.40 -70.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: PHO000099 RELATED DB: TARGETDB DBREF 1VDX A 1 184 UNP O57823 Y099_PYRHO 1 184 SEQRES 1 A 184 MET ARG ALA PHE ILE ALA ILE ASP VAL ASN GLU SER VAL SEQRES 2 A 184 ARG ASP SER LEU VAL ARG ALA GLN ASP TYR ILE GLY SER SEQRES 3 A 184 LYS GLU ALA LYS ILE LYS PHE VAL GLU ARG GLU ASN LEU SEQRES 4 A 184 HIS ILE THR LEU LYS PHE LEU GLY GLU ILE THR GLU GLU SEQRES 5 A 184 GLN ALA GLU GLU ILE LYS ASN ILE LEU LYS LYS ILE ALA SEQRES 6 A 184 GLU LYS TYR LYS LYS HIS GLU VAL LYS VAL LYS GLY ILE SEQRES 7 A 184 GLY VAL PHE PRO ASN PRO ASN TYR ILE ARG VAL ILE TRP SEQRES 8 A 184 ALA GLY ILE GLU ASN ASP GLU ILE ILE ARG GLU MET ALA SEQRES 9 A 184 ARG GLU ILE GLU ASP GLU LEU ALA LYS LEU GLY PHE LYS SEQRES 10 A 184 LYS GLU GLY ASN PHE VAL ALA HIS ILE THR LEU GLY ARG SEQRES 11 A 184 VAL LYS PHE VAL LYS ASP LYS LEU GLY LEU THR MET LYS SEQRES 12 A 184 LEU LYS GLU LEU ALA ASN GLU ASP PHE GLY SER PHE VAL SEQRES 13 A 184 VAL ASP ALA ILE GLU LEU LYS LYS SER THR LEU THR PRO SEQRES 14 A 184 LYS GLY PRO ILE TYR GLU THR LEU ALA ARG PHE GLU LEU SEQRES 15 A 184 SER GLU HET CL A 185 1 HETNAM CL CHLORIDE ION FORMUL 2 CL CL 1- FORMUL 3 HOH *41(H2 O) HELIX 1 1 ASN A 10 GLY A 25 1 16 HELIX 2 2 GLU A 35 ASN A 38 5 4 HELIX 3 3 THR A 50 GLU A 66 1 17 HELIX 4 4 ASP A 97 LYS A 113 1 17 HELIX 5 5 ASP A 136 GLU A 146 1 11 SHEET 1 A 4 HIS A 40 GLU A 48 0 SHEET 2 A 4 ARG A 2 ASP A 8 -1 N ILE A 5 O LEU A 43 SHEET 3 A 4 ALA A 159 THR A 168 -1 O LYS A 163 N PHE A 4 SHEET 4 A 4 GLY A 171 GLU A 181 -1 O ILE A 173 N THR A 166 SHEET 1 B 5 ALA A 29 PHE A 33 0 SHEET 2 B 5 HIS A 125 VAL A 134 -1 O ARG A 130 N LYS A 32 SHEET 3 B 5 ILE A 87 GLU A 95 -1 N ILE A 90 O GLY A 129 SHEET 4 B 5 HIS A 71 PRO A 82 -1 N LYS A 74 O GLU A 95 SHEET 5 B 5 ASP A 151 VAL A 157 -1 O GLY A 153 N VAL A 75 CISPEP 1 PHE A 81 PRO A 82 0 -3.00 CRYST1 44.068 45.471 93.171 90.00 90.00 90.00 P 21 21 21 4 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 0.022692 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010733 0.00000