HEADER OXIDOREDUCTASE 04-OCT-18 6MOS TITLE STRUCTURE OF THIOREDOXIN 1 FROM THE THERMOPHILIC EUBACTERIUM TITLE 2 THERMOSIPHO AFRICANUS TCF52B COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOSIPHO AFRICANUS (STRAIN TCF52B); SOURCE 3 ORGANISM_TAXID: 484019; SOURCE 4 STRAIN: TCF52B; SOURCE 5 GENE: THA_37; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: BL21-CODONPLUS-RIL KEYWDS THIOREDOXIN, THERMOPHILE, THERMOSIPHO AFRICANUS, PROTEIN STABILITY, KEYWDS 2 CATALYSIS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR N.SAHTOUT,J.R.KUTTIYATVEETIL,D.A.R.SANDERS REVDAT 2 06-MAR-24 6MOS 1 REMARK REVDAT 1 14-AUG-19 6MOS 0 JRNL AUTH N.SAHTOUT,J.R.A.KUTTIYATVEETIL,D.A.R.SANDERS JRNL TITL STRUCTURE AND FUNCTION OF THE PUTATIVE THIOREDOXIN 1 FROM JRNL TITL 2 THE THERMOPHILIC EUBACTERIUM THERMOSIPHO AFRICANUS STRAIN JRNL TITL 3 TCF52B. JRNL REF BIOCHIM BIOPHYS ACTA V.1867 426 2019 JRNL REF 2 PROTEINS PROTEOM JRNL REFN ISSN 1878-1454 JRNL PMID 30716506 JRNL DOI 10.1016/J.BBAPAP.2019.01.011 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.SAHTOUT,J.R.KUTTIYATVEETIL,M.FODJE,D.A.SANDERS REMARK 1 TITL PUTATIVE THIOREDOXIN TRX1 FROM THERMOSIPHO AFRICANUS STRAIN REMARK 1 TITL 2 TCF52B: EXPRESSION, PURIFICATION AND STRUCTURAL REMARK 1 TITL 3 DETERMINATION USING S-SAD. REMARK 1 REF ACTA CRYSTALLOGR F STRUCT V. 72 443 2016 REMARK 1 REF 2 BIOL COMMUN REMARK 1 REFN ESSN 2053-230X REMARK 1 PMID 27303896 REMARK 1 DOI 10.1107/S2053230X16007214 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.336 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 8944 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.841 REMARK 3 FREE R VALUE TEST SET COUNT : 433 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 33.0622 - 2.5960 1.00 2964 156 0.2051 0.2305 REMARK 3 2 2.5960 - 2.0606 1.00 2819 142 0.2370 0.2782 REMARK 3 3 2.0606 - 1.8001 0.97 2728 135 0.1905 0.2753 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.155 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.845 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.006 761 REMARK 3 ANGLE : 0.843 1028 REMARK 3 CHIRALITY : 0.054 120 REMARK 3 PLANARITY : 0.004 127 REMARK 3 DIHEDRAL : 11.295 485 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6MOS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000236149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8989 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 41.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.300 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: LARGE IRREGULAR-SHAPED TRAPEZOID CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2 , 0.1 M BIS-TRIS PH 6.5, REMARK 280 25%(W/V) PEG 3350, MICROBATCH, TEMPERATURE 289K 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 20.22700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.91100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.51150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.91100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.22700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.51150 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 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 SER A 2 REMARK 465 TYR A 3 REMARK 465 TYR A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 ASP A 11 REMARK 465 TYR A 12 REMARK 465 ASP A 13 REMARK 465 ILE A 14 REMARK 465 PRO A 15 REMARK 465 THR A 16 REMARK 465 THR A 17 REMARK 465 GLU A 18 REMARK 465 ASN A 19 REMARK 465 LEU A 20 REMARK 465 TYR A 21 REMARK 465 PHE A 22 REMARK 465 GLN A 23 REMARK 465 GLY A 24 REMARK 465 ALA A 25 REMARK 465 MET A 26 REMARK 465 ALA A 27 REMARK 465 GLU A 117 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 ARG A 96 -66.91 72.25 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 TAM A 201 DBREF 6MOS A 28 117 UNP B7IEN1 B7IEN1_THEAB 1 90 SEQADV 6MOS MET A 1 UNP B7IEN1 INITIATING METHIONINE SEQADV 6MOS SER A 2 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS TYR A 3 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS TYR A 4 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS HIS A 5 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS HIS A 6 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS HIS A 7 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS HIS A 8 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS HIS A 9 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS HIS A 10 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS ASP A 11 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS TYR A 12 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS ASP A 13 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS ILE A 14 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS PRO A 15 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS THR A 16 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS THR A 17 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS GLU A 18 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS ASN A 19 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS LEU A 20 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS TYR A 21 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS PHE A 22 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS GLN A 23 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS GLY A 24 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS ALA A 25 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS MET A 26 UNP B7IEN1 EXPRESSION TAG SEQADV 6MOS ALA A 27 UNP B7IEN1 EXPRESSION TAG SEQRES 1 A 117 MET SER TYR TYR HIS HIS HIS HIS HIS HIS ASP TYR ASP SEQRES 2 A 117 ILE PRO THR THR GLU ASN LEU TYR PHE GLN GLY ALA MET SEQRES 3 A 117 ALA MET LYS ILE GLU TYR PHE LYS ASN ASP LYS CYS SER SEQRES 4 A 117 VAL CYS LYS ALA MET LEU PRO LYS ILE GLN THR ILE ALA SEQRES 5 A 117 LYS ASN PHE ASP ILE ASP ILE GLU VAL ILE ASP VAL ILE SEQRES 6 A 117 GLU ASN PRO SER TYR PRO ALA GLN LYS LEU VAL PHE THR SEQRES 7 A 117 VAL PRO THR VAL ILE ILE LEU ASP LYS GLU PHE GLU ILE SEQRES 8 A 117 LYS ARG PHE ALA ARG ASN PHE SER ILE SER GLU VAL ILE SEQRES 9 A 117 ASN THR ILE GLU ARG TYR LEU GLU ILE SER ASN LYS GLU HET TAM A 201 11 HETNAM TAM TRIS(HYDROXYETHYL)AMINOMETHANE FORMUL 2 TAM C7 H17 N O3 FORMUL 3 HOH *21(H2 O) HELIX 1 AA1 CYS A 38 ASP A 56 1 19 HELIX 2 AA2 PRO A 68 LYS A 74 1 7 HELIX 3 AA3 SER A 99 LYS A 116 1 18 SHEET 1 AA1 4 ASP A 58 ASP A 63 0 SHEET 2 AA1 4 LYS A 29 LYS A 34 1 N TYR A 32 O ILE A 62 SHEET 3 AA1 4 THR A 81 ASP A 86 -1 O LEU A 85 N LYS A 29 SHEET 4 AA1 4 PHE A 89 ALA A 95 -1 O PHE A 94 N VAL A 82 SSBOND 1 CYS A 38 CYS A 41 1555 1555 2.09 CISPEP 1 VAL A 79 PRO A 80 0 -1.98 SITE 1 AC1 7 ASN A 35 ILE A 59 GLU A 60 VAL A 61 SITE 2 AC1 7 THR A 78 VAL A 79 HOH A 301 CRYST1 40.454 41.023 55.822 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 0.024719 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024377 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017914 0.00000