HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 20-APR-07 2YWO TITLE CRYSTAL STRUCTURE OF REDUCED THIOREDOXIN-LIKE PROTEIN FROM THERMUS TITLE 2 THERMOPHILUS HB8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE THIOL-DISULFIDE ISOMERASE/THIOREDOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: THIOREDOXIN-LIKE PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-11A KEYWDS REDOX PROTEIN, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND KEYWDS 2 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 3 INITIATIVE, RSGI, STRUCTURAL GENOMICS, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR A.EBIHARA,M.MANZOKU,S.YOKOYAMA,S.KURAMITSU,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 6 15-NOV-23 2YWO 1 REMARK REVDAT 5 25-OCT-23 2YWO 1 LINK REVDAT 4 11-OCT-17 2YWO 1 REMARK REVDAT 3 13-JUL-11 2YWO 1 VERSN REVDAT 2 24-FEB-09 2YWO 1 VERSN REVDAT 1 23-OCT-07 2YWO 0 JRNL AUTH A.EBIHARA,M.MANZOKU,S.YOKOYAMA,S.KURAMITSU JRNL TITL CRYSTAL STRUCTURE OF REDUCED THIOREDOXIN-LIKE PROTEIN FROM JRNL TITL 2 THERMUS THERMOPHILUS HB8 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1683694.890 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 21703 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) : 0.215 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2160 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3136 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 366 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1508 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 143 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.04000 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.110 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) : 1.290 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.870 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.130 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.160 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 19.89 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.PARAM REMARK 3 PARAMETER FILE 2 : WATER.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 2YWO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000027228. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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) : 1.0000 REMARK 200 MONOCHROMATOR : SI DOUBLE-CRYSTAL 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21756 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 59.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.30 REMARK 200 R MERGE FOR SHELL (I) : 0.21900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 12.80 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: PDB ENTRY 2CVB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 ACETATE, 32% PEG MME 2000, PH 4.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 48.81000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.74500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.74500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.40500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.74500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.74500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 73.21500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.74500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.74500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.40500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.74500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.74500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 73.21500 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 48.81000 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 GLU A 10 -1.08 77.82 REMARK 500 ASP A 103 75.67 -106.75 REMARK 500 ASN A 138 69.58 -159.41 REMARK 500 HIS A 148 78.59 -107.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003001681.2 RELATED DB: TARGETDB DBREF 2YWO A 1 188 UNP Q5SKQ0 Q5SKQ0_THET8 1 188 SEQRES 1 A 188 MSE LEU GLN TYR PRO GLU LEU PRO LEU GLU SER PRO LEU SEQRES 2 A 188 ILE ASP ALA GLU LEU PRO ASP PRO ARG GLY GLY ARG TYR SEQRES 3 A 188 ARG LEU SER GLN PHE HIS GLU PRO LEU LEU ALA VAL VAL SEQRES 4 A 188 PHE MSE CYS ASN HIS CYS PRO TYR VAL LYS GLY SER ILE SEQRES 5 A 188 GLY GLU LEU VAL ALA LEU ALA GLU ARG TYR ARG GLY LYS SEQRES 6 A 188 VAL ALA PHE VAL GLY ILE ASN ALA ASN ASP TYR GLU LYS SEQRES 7 A 188 TYR PRO GLU ASP ALA PRO GLU LYS MSE ALA ALA PHE ALA SEQRES 8 A 188 GLU GLU HIS GLY ILE PHE PHE PRO TYR LEU LEU ASP GLU SEQRES 9 A 188 THR GLN GLU VAL ALA LYS ALA TYR ARG ALA LEU ARG THR SEQRES 10 A 188 PRO GLU VAL PHE LEU PHE ASP GLU ARG ARG LEU LEU ARG SEQRES 11 A 188 TYR HIS GLY ARG VAL ASN ASP ASN PRO LYS ASP PRO SER SEQRES 12 A 188 LYS VAL GLN SER HIS ASP LEU GLU ALA ALA ILE GLU ALA SEQRES 13 A 188 LEU LEU ARG GLY GLU GLU PRO PRO LEU LYS GLU ALA PRO SEQRES 14 A 188 ALA ILE GLY CYS THR ILE LYS TRP ARG PRO GLY ASN GLU SEQRES 15 A 188 PRO GLU VAL ARG ILE GLY MODRES 2YWO MSE A 1 MET SELENOMETHIONINE MODRES 2YWO MSE A 41 MET SELENOMETHIONINE MODRES 2YWO MSE A 87 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 41 8 HET MSE A 87 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *143(H2 O) HELIX 1 1 SER A 29 PHE A 31 5 3 HELIX 2 2 CYS A 45 GLY A 50 1 6 HELIX 3 3 SER A 51 TYR A 62 1 12 HELIX 4 4 TYR A 79 ASP A 82 5 4 HELIX 5 5 ALA A 83 HIS A 94 1 12 HELIX 6 6 GLN A 106 TYR A 112 1 7 HELIX 7 7 ASP A 141 VAL A 145 5 5 HELIX 8 8 HIS A 148 ARG A 159 1 12 SHEET 1 A 2 GLU A 17 PRO A 19 0 SHEET 2 A 2 ARG A 25 ARG A 27 -1 O TYR A 26 N LEU A 18 SHEET 1 B 5 TYR A 100 LEU A 102 0 SHEET 2 B 5 VAL A 66 ASN A 72 1 N GLY A 70 O LEU A 101 SHEET 3 B 5 LEU A 35 MSE A 41 1 N ALA A 37 O ALA A 67 SHEET 4 B 5 GLU A 119 PHE A 123 -1 O PHE A 121 N VAL A 38 SHEET 5 B 5 LEU A 129 GLY A 133 -1 O TYR A 131 N LEU A 122 SHEET 1 C 2 ARG A 116 THR A 117 0 SHEET 2 C 2 CYS A 173 THR A 174 -1 O CYS A 173 N THR A 117 LINK C MSE A 1 N LEU A 2 1555 1555 1.33 LINK C PHE A 40 N MSE A 41 1555 1555 1.33 LINK C MSE A 41 N CYS A 42 1555 1555 1.33 LINK C LYS A 86 N MSE A 87 1555 1555 1.33 LINK C MSE A 87 N ALA A 88 1555 1555 1.33 CISPEP 1 THR A 117 PRO A 118 0 -0.21 CRYST1 73.490 73.490 97.620 90.00 90.00 90.00 P 41 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 0.013607 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010244 0.00000 HETATM 1 N MSE A 1 43.915 25.427 15.387 1.00 49.87 N HETATM 2 CA MSE A 1 43.852 24.559 16.601 1.00 49.47 C HETATM 3 C MSE A 1 42.658 23.604 16.541 1.00 45.46 C HETATM 4 O MSE A 1 41.731 23.809 15.755 1.00 43.61 O HETATM 5 CB MSE A 1 43.780 25.419 17.866 1.00 55.97 C HETATM 6 CG MSE A 1 42.546 26.305 17.958 1.00 63.35 C HETATM 7 SE MSE A 1 42.498 27.325 19.599 1.00 75.04 SE HETATM 8 CE MSE A 1 41.998 25.906 20.816 1.00 70.91 C