HEADER ELECTRON TRANSPORT 04-JUN-05 2CVK TITLE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS THIOREDOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS TRX, STRUCTURAL GENOMICS, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 2 INITIATIVE, RSGI, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR H.YANAI,S.YOKOYAMA,S.KURAMITSU,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 4 15-NOV-23 2CVK 1 REMARK REVDAT 3 25-OCT-23 2CVK 1 LINK REVDAT 2 24-FEB-09 2CVK 1 VERSN REVDAT 1 04-DEC-05 2CVK 0 JRNL AUTH H.YANAI,S.YOKOYAMA,S.KURAMITSU JRNL TITL CRYSTAL STRUCTURE OF A REDUCED THIOREDOXIN FROM THERMUS JRNL TITL 2 THERMOPHILUS HB8 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1065761.320 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 7458 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) : 0.232 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.800 REMARK 3 FREE R VALUE TEST SET COUNT : 803 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1080 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 133 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 844 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.43000 REMARK 3 B22 (A**2) : -2.43000 REMARK 3 B33 (A**2) : 4.86000 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.10 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 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) : 1.700 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.650 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.570 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.910 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 54.65 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CVK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000024670. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97903, 0.90000, 0.97939 REMARK 200 MONOCHROMATOR : SI DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : 0.03800 REMARK 200 FOR THE DATA SET : 24.3000 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.11600 REMARK 200 R SYM FOR SHELL (I) : 0.10400 REMARK 200 FOR SHELL : 19.54 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1NSW(CHAIN:D) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.3M SODIUM CHLORIDE, 0.1M HEPES, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 29.80500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.42500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.70750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.42500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.42500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.90250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.42500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.42500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.70750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.42500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.42500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 14.90250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 29.80500 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 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 MSE A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 108 REMARK 465 THR A 109 REMARK 465 ALA A 110 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003000408.1 RELATED DB: TARGETDB DBREF 2CVK A 1 110 UNP Q72HU9 Q72HU9_THET2 1 110 SEQRES 1 A 110 MSE ALA LYS PRO ILE GLU VAL THR ASP GLN ASN PHE ASP SEQRES 2 A 110 GLU THR LEU GLY GLN HIS PRO LEU VAL LEU VAL ASP PHE SEQRES 3 A 110 TRP ALA GLU TRP CYS ALA PRO CYS ARG MSE ILE ALA PRO SEQRES 4 A 110 ILE LEU GLU GLU ILE ALA LYS GLU TYR GLU GLY LYS LEU SEQRES 5 A 110 LEU VAL ALA LYS LEU ASP VAL ASP GLU ASN PRO LYS THR SEQRES 6 A 110 ALA MSE ARG TYR ARG VAL MSE SER ILE PRO THR VAL ILE SEQRES 7 A 110 LEU PHE LYS ASP GLY GLN PRO VAL GLU VAL LEU VAL GLY SEQRES 8 A 110 ALA GLN PRO LYS ARG ASN TYR GLN ALA LYS ILE GLU LYS SEQRES 9 A 110 HIS LEU PRO ALA THR ALA MODRES 2CVK MSE A 36 MET SELENOMETHIONINE MODRES 2CVK MSE A 67 MET SELENOMETHIONINE MODRES 2CVK MSE A 72 MET SELENOMETHIONINE HET MSE A 36 8 HET MSE A 67 8 HET MSE A 72 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *43(H2 O) HELIX 1 1 ASN A 11 HIS A 19 1 9 HELIX 2 2 CYS A 31 TYR A 48 1 18 HELIX 3 3 ASN A 62 ARG A 70 1 9 HELIX 4 4 PRO A 94 LYS A 104 1 11 SHEET 1 A 5 ILE A 5 GLU A 6 0 SHEET 2 A 5 LEU A 53 ASP A 58 1 O VAL A 54 N ILE A 5 SHEET 3 A 5 LEU A 21 TRP A 27 1 N LEU A 23 O ALA A 55 SHEET 4 A 5 THR A 76 LYS A 81 -1 O THR A 76 N PHE A 26 SHEET 5 A 5 GLN A 84 VAL A 90 -1 O VAL A 86 N LEU A 79 LINK C ARG A 35 N MSE A 36 1555 1555 1.33 LINK C MSE A 36 N ILE A 37 1555 1555 1.33 LINK C ALA A 66 N MSE A 67 1555 1555 1.33 LINK C MSE A 67 N ARG A 68 1555 1555 1.33 LINK C VAL A 71 N MSE A 72 1555 1555 1.33 LINK C MSE A 72 N SER A 73 1555 1555 1.33 CISPEP 1 ILE A 74 PRO A 75 0 -0.09 CRYST1 58.850 58.850 59.610 90.00 90.00 90.00 P 43 21 2 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 0.016992 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016776 0.00000