HEADER HYDROLASE 01-DEC-03 1VH2 TITLE CRYSTAL STRUCTURE OF A AUTOINDUCER-2 SYNTHESIS PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-RIBOSYLHOMOCYSTEINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AUTOINDUCER-2 PRODUCTION PROTEIN LUXS, AI-2 SYNTHESIS COMPND 5 PROTEIN; COMPND 6 EC: 3.13.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 1299; SOURCE 4 GENE: LUXS, DR2387; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURAL GENOMICS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR STRUCTURAL GENOMIX REVDAT 5 27-DEC-23 1VH2 1 REMARK LINK REVDAT 4 13-JUL-11 1VH2 1 VERSN REVDAT 3 24-FEB-09 1VH2 1 VERSN REVDAT 2 30-AUG-05 1VH2 1 JRNL REVDAT 1 30-DEC-03 1VH2 0 JRNL AUTH J.BADGER,J.M.SAUDER,J.M.ADAMS,S.ANTONYSAMY,K.BAIN, JRNL AUTH 2 M.G.BERGSEID,S.G.BUCHANAN,M.D.BUCHANAN,Y.BATIYENKO, JRNL AUTH 3 J.A.CHRISTOPHER,S.EMTAGE,A.EROSHKINA,I.FEIL,E.B.FURLONG, JRNL AUTH 4 K.S.GAJIWALA,X.GAO,D.HE,J.HENDLE,A.HUBER,K.HODA,P.KEARINS, JRNL AUTH 5 C.KISSINGER,B.LAUBERT,H.A.LEWIS,J.LIN,K.LOOMIS,D.LORIMER, JRNL AUTH 6 G.LOUIE,M.MALETIC,C.D.MARSH,I.MILLER,J.MOLINARI, JRNL AUTH 7 H.J.MULLER-DIECKMANN,J.M.NEWMAN,B.W.NOLAND,B.PAGARIGAN, JRNL AUTH 8 F.PARK,T.S.PEAT,K.W.POST,S.RADOJICIC,A.RAMOS,R.ROMERO, JRNL AUTH 9 M.E.RUTTER,W.E.SANDERSON,K.D.SCHWINN,J.TRESSER,J.WINHOVEN, JRNL AUTH10 T.A.WRIGHT,L.WU,J.XU,T.J.HARRIS JRNL TITL STRUCTURAL ANALYSIS OF A SET OF PROTEINS RESULTING FROM A JRNL TITL 2 BACTERIAL GENOMICS PROJECT JRNL REF PROTEINS V. 60 787 2005 JRNL REFN ISSN 0887-3585 JRNL PMID 16021622 JRNL DOI 10.1002/PROT.20541 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 4.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 10927 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1122 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1170 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 80 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.26400 REMARK 3 B22 (A**2) : 0.05600 REMARK 3 B33 (A**2) : -0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.27900 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.009 ; NULL REMARK 3 ANGLE DISTANCE (A) : 1.682 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.007 ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.121 ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 1.638 ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.708 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.734 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 5.938 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.574 ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VH2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000001861. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 32-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10942 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 40.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.07100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 31.90 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 25.41000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.85500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.41000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.85500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -89.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 32.06952 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 46.19999 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 PRO A 2 REMARK 465 ASP A 3 REMARK 465 MET A 4 REMARK 465 ALA A 5 REMARK 465 ASN A 6 REMARK 465 GLY A 159 REMARK 465 SER A 160 REMARK 465 HIS A 161 REMARK 465 HIS A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 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 GLU A 157 CD OE1 OE2 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 SER A 9 91.76 -163.26 REMARK 500 ASP A 95 71.58 -151.43 REMARK 500 ASN A 127 60.65 -155.51 REMARK 500 ASP A 130 75.19 -100.86 REMARK 500 ASP A 132 88.74 -155.24 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 ZN A 167 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 57 NE2 REMARK 620 2 HIS A 61 NE2 108.7 REMARK 620 3 CYS A 125 SG 99.2 114.6 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 ZN A 167 DBREF 1VH2 A 1 158 UNP Q9RRU8 LUXS_DEIRA 1 158 SEQADV 1VH2 GLY A 159 UNP Q9RRU8 CLONING ARTIFACT SEQADV 1VH2 SER A 160 UNP Q9RRU8 CLONING ARTIFACT SEQADV 1VH2 HIS A 161 UNP Q9RRU8 CLONING ARTIFACT SEQADV 1VH2 HIS A 162 UNP Q9RRU8 CLONING ARTIFACT SEQADV 1VH2 HIS A 163 UNP Q9RRU8 CLONING ARTIFACT SEQADV 1VH2 HIS A 164 UNP Q9RRU8 CLONING ARTIFACT SEQADV 1VH2 HIS A 165 UNP Q9RRU8 CLONING ARTIFACT SEQADV 1VH2 HIS A 166 UNP Q9RRU8 CLONING ARTIFACT SEQRES 1 A 166 MET PRO ASP MET ALA ASN VAL GLU SER PHE ASP LEU ASP SEQRES 2 A 166 HIS THR LYS VAL LYS ALA PRO TYR VAL ARG LEU ALA GLY SEQRES 3 A 166 VAL LYS THR THR PRO LYS GLY ASP GLN ILE SER LYS TYR SEQRES 4 A 166 ASP LEU ARG PHE LEU GLN PRO ASN GLN GLY ALA ILE ASP SEQRES 5 A 166 PRO ALA ALA ILE HIS THR LEU GLU HIS LEU LEU ALA GLY SEQRES 6 A 166 TYR MET ARG ASP HIS LEU GLU GLY VAL VAL ASP VAL SER SEQRES 7 A 166 PRO MET GLY CYS ARG THR GLY MET TYR MET ALA VAL ILE SEQRES 8 A 166 GLY GLU PRO ASP GLU GLN GLY VAL MET LYS ALA PHE GLU SEQRES 9 A 166 ALA ALA LEU LYS ASP THR ALA GLY HIS ASP GLN PRO ILE SEQRES 10 A 166 PRO GLY VAL SER GLU LEU GLU CYS GLY ASN TYR ARG ASP SEQRES 11 A 166 HIS ASP LEU ALA ALA ALA ARG GLN HIS ALA ARG ASP VAL SEQRES 12 A 166 LEU ASP GLN GLY LEU LYS VAL GLN GLU THR ILE LEU LEU SEQRES 13 A 166 GLU ARG GLY SER HIS HIS HIS HIS HIS HIS HET ZN A 167 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *80(H2 O) HELIX 1 1 ASP A 52 LEU A 71 1 20 HELIX 2 2 ASP A 95 GLY A 112 1 18 HELIX 3 3 ASP A 132 GLY A 147 1 16 SHEET 1 A 4 TYR A 21 THR A 29 0 SHEET 2 A 4 GLN A 35 ARG A 42 -1 O LYS A 38 N GLY A 26 SHEET 3 A 4 GLY A 85 ILE A 91 -1 O VAL A 90 N SER A 37 SHEET 4 A 4 VAL A 74 PRO A 79 -1 N SER A 78 O TYR A 87 LINK NE2 HIS A 57 ZN ZN A 167 1555 1555 2.22 LINK NE2 HIS A 61 ZN ZN A 167 1555 1555 2.17 LINK SG CYS A 125 ZN ZN A 167 1555 1555 2.29 CISPEP 1 ALA A 19 PRO A 20 0 -0.07 SITE 1 AC1 3 HIS A 57 HIS A 61 CYS A 125 CRYST1 50.820 69.710 49.860 90.00 112.09 90.00 C 1 2 1 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 0.019677 0.000000 0.007986 0.00000 SCALE2 0.000000 0.014345 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021645 0.00000