HEADER UNKNOWN FUNCTION 20-JAN-10 3LGC TITLE CRYSTAL STRUCTURE OF GLUTAREDOXIN 1 FROM FRANCISELLA TULARENSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAREDOXIN 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FRANCISELLA TULARENSIS SUBSP. TULARENSIS; SOURCE 3 ORGANISM_TAXID: 177416; SOURCE 4 STRAIN: SCHU S4; SOURCE 5 GENE: FTT0533C, FTT_0533C, GRXA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS ALPHA-BETA SANDWICH, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS OF KEYWDS 2 INFECTIOUS DISEASES, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS KEYWDS 3 DISEASES, CSGID, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR N.MALTSEVA,Y.KIM,L.PAPAZISI,W.F.ANDERSON,A.JOACHIMIAK,CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID) REVDAT 2 01-NOV-17 3LGC 1 REMARK REVDAT 1 16-FEB-10 3LGC 0 JRNL AUTH N.MALTSEVA,Y.KIM,L.PAPAZISI,W.F.ANDERSON,A.JOACHIMIAK JRNL TITL CRYSTAL STRUCTURE OF GLUTAREDOXIN 1 FROM FRANCISELLA JRNL TITL 2 TULARENSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.4_147) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 4075 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.520 REMARK 3 FREE R VALUE TEST SET COUNT : 184 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 33.2209 - 2.7682 1.00 3891 184 0.1752 0.2227 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.26 REMARK 3 B_SOL : 8.08 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.89930 REMARK 3 B22 (A**2) : -4.89930 REMARK 3 B33 (A**2) : 3.75440 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 : 0.014 794 REMARK 3 ANGLE : 1.462 1075 REMARK 3 CHIRALITY : 0.090 111 REMARK 3 PLANARITY : 0.008 139 REMARK 3 DIHEDRAL : 20.029 287 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 38.1741 7.7438 6.5028 REMARK 3 T TENSOR REMARK 3 T11: 0.0858 T22: 0.0387 REMARK 3 T33: 0.0538 T12: -0.0229 REMARK 3 T13: 0.0130 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 1.8049 L22: 1.8641 REMARK 3 L33: 1.2523 L12: -1.4734 REMARK 3 L13: -0.0055 L23: -0.6014 REMARK 3 S TENSOR REMARK 3 S11: 0.0223 S12: -0.1764 S13: 0.1764 REMARK 3 S21: -0.1845 S22: -0.1382 S23: -0.1629 REMARK 3 S31: 0.0961 S32: 0.0626 S33: 0.0950 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 3LGC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000057243. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4103 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.770 REMARK 200 RESOLUTION RANGE LOW (A) : 33.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.17500 REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.84700 REMARK 200 FOR SHELL : 6.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000, MLPHARE, SOLVE, SHELX, DM, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE, 0.1 M TRIS REMARK 280 PH 8.5, 20 % PEG 8000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 21.03867 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 42.07733 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 31.55800 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 52.59667 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 10.51933 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ILE A 56 -88.38 -77.58 REMARK 500 SER A 57 -9.33 87.84 REMARK 500 SER A 57 18.18 -155.82 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 SO4 A 91 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 92 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 93 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: IDP01801 RELATED DB: TARGETDB DBREF 3LGC A 1 86 UNP Q5NHD0 Q5NHD0_FRATT 1 86 SEQADV 3LGC SER A -2 UNP Q5NHD0 EXPRESSION TAG SEQADV 3LGC ASN A -1 UNP Q5NHD0 EXPRESSION TAG SEQADV 3LGC ALA A 0 UNP Q5NHD0 EXPRESSION TAG SEQRES 1 A 89 SER ASN ALA MSE LYS VAL LYS ILE TYR THR ARG ASN GLY SEQRES 2 A 89 CYS PRO TYR CYS VAL TRP ALA LYS GLN TRP PHE GLU GLU SEQRES 3 A 89 ASN ASN ILE ALA PHE ASP GLU THR ILE ILE ASP ASP TYR SEQRES 4 A 89 ALA GLN ARG SER LYS PHE TYR ASP GLU MSE ASN GLN SER SEQRES 5 A 89 GLY LYS VAL ILE PHE PRO ILE SER THR VAL PRO GLN ILE SEQRES 6 A 89 PHE ILE ASP ASP GLU HIS ILE GLY GLY PHE THR GLU LEU SEQRES 7 A 89 LYS ALA ASN ALA ASP LYS ILE LEU ASN LYS LYS MODRES 3LGC MSE A 1 MET SELENOMETHIONINE MODRES 3LGC MSE A 46 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 46 8 HET SO4 A 91 5 HET GOL A 92 6 HET SO4 A 93 5 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 SO4 2(O4 S 2-) FORMUL 3 GOL C3 H8 O3 FORMUL 5 HOH *30(H2 O) HELIX 1 1 CYS A 11 ASN A 24 1 14 HELIX 2 2 ASP A 35 GLY A 50 1 16 HELIX 3 3 GLY A 71 ASN A 78 1 8 HELIX 4 4 ASN A 78 ASN A 84 1 7 SHEET 1 A 4 ASP A 29 ILE A 32 0 SHEET 2 A 4 VAL A 3 THR A 7 1 N VAL A 3 O ASP A 29 SHEET 3 A 4 GLN A 61 ILE A 64 -1 O PHE A 63 N LYS A 4 SHEET 4 A 4 GLU A 67 GLY A 70 -1 O ILE A 69 N ILE A 62 SSBOND 1 CYS A 11 CYS A 14 1555 1555 2.03 LINK C ALA A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N LYS A 2 1555 1555 1.34 LINK C GLU A 45 N MSE A 46 1555 1555 1.32 LINK C MSE A 46 N ASN A 47 1555 1555 1.33 CISPEP 1 VAL A 59 PRO A 60 0 10.41 SITE 1 AC1 5 ASP A 29 ASP A 34 ASP A 35 HOH A 94 SITE 2 AC1 5 HOH A 113 SITE 1 AC2 6 PRO A 60 GLY A 71 PHE A 72 THR A 73 SITE 2 AC2 6 GLU A 74 HOH A 90 SITE 1 AC3 4 ARG A 8 LYS A 18 GLU A 30 ILE A 32 CRYST1 66.437 66.437 63.116 90.00 90.00 120.00 P 61 6 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 0.015052 0.008690 0.000000 0.00000 SCALE2 0.000000 0.017380 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015844 0.00000