HEADER OXIDOREDUCTASE 07-JUL-20 6ZOM TITLE OXIDIZED THIOREDOXIN 1 FROM THE ANAEROBIC BACTERIA DESULFOVIBRIO TITLE 2 VULGARIS HILDENBOROUGH COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: OXIDIZED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS; SOURCE 3 ORGANISM_TAXID: 881; SOURCE 4 GENE: TRX, DVU_1839; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS THIOREDOXIN, DESULFOVIBRIO, ENZYME, CYSTEIN, VULGARIS, REDOX KEYWDS 2 HOMEOSTASIS, REGULATION, THIOL, OXIDIZED, OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.GARCIN,O.BORNET,M.NOUAILLER,L.PIEULLE,F.GUERLESQUIN,C.SEBBAN- AUTHOR 2 KREUZER REVDAT 2 14-JUN-23 6ZOM 1 REMARK REVDAT 1 14-JUL-21 6ZOM 0 JRNL AUTH H.GAUSSIER,M.NOUAILLER,E.CHAMPAUD,E.B.GARCIN, JRNL AUTH 2 C.SEBBAN-KREUZER,O.BORNET,M.GAREL,C.TAMBURINI,L.PIEULLE, JRNL AUTH 3 A.DOLLA,N.PRADEL JRNL TITL GLUTAMATE OPTIMIZES ENZYMATIC ACTIVITY UNDER HIGH JRNL TITL 2 HYDROSTATIC PRESSURE IN DESULFOVIBRIO SPECIES: EFFECTS ON JRNL TITL 3 THE UBIQUITOUS THIOREDOXIN SYSTEM. JRNL REF EXTREMOPHILES V. 25 385 2021 JRNL REFN ESSN 1433-4909 JRNL PMID 34196828 JRNL DOI 10.1007/S00792-021-01236-X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.B.GARCIN,O.BORNET,L.PIEULLE,F.GUERLESQUIN,C.SEBBAN-KREUZER REMARK 1 TITL 1H, 13C AND 15N CHEMICAL SHIFT ASSIGNMENTS OF THE REMARK 1 TITL 2 THIOREDOXIN FROM THE OBLIGATE ANAEROBE DESULFOVIBRIO REMARK 1 TITL 3 VULGARIS HILDENBOROUGH. REMARK 1 REF BIOMOL NMR ASSIGN V. 5 177 2011 REMARK 1 REFN ESSN 1874-270X REMARK 1 DOI 10.1007/S12104-011-9294-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6ZOM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292109811. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 290 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-99% 13C; U-99% 15N] REMARK 210 THIOREDOXIN 1, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D REMARK 210 HNCACB; 3D HCCH-TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D HNHA; 3D HBHA(CO)NH; REMARK 210 3D HN(CO)CA; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA, TALOS, TOPSPIN, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 71 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG A 34 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 71 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 1 ARG A 71 -93.29 -94.31 REMARK 500 1 ALA A 72 79.31 -156.51 REMARK 500 1 ASN A 81 15.45 53.53 REMARK 500 2 ARG A 71 -93.54 -92.80 REMARK 500 2 ALA A 72 81.45 -157.78 REMARK 500 2 PRO A 74 95.95 -69.71 REMARK 500 2 ASN A 81 14.21 53.15 REMARK 500 2 VAL A 85 -32.91 -133.12 REMARK 500 3 ARG A 71 -92.53 -96.66 REMARK 500 3 ALA A 72 86.10 -155.83 REMARK 500 3 ASN A 81 16.39 52.90 REMARK 500 4 ARG A 71 -88.12 -92.41 REMARK 500 4 ALA A 72 80.72 -157.95 REMARK 500 4 ASN A 81 17.83 52.32 REMARK 500 4 VAL A 85 -34.05 -130.01 REMARK 500 4 LYS A 104 -76.46 -116.83 REMARK 500 5 ARG A 71 -90.64 -100.10 REMARK 500 5 ALA A 72 73.85 -151.87 REMARK 500 5 ASN A 81 -8.56 56.58 REMARK 500 5 LYS A 104 -62.98 -93.73 REMARK 500 6 ARG A 71 -93.24 -93.79 REMARK 500 6 ALA A 72 77.29 -157.20 REMARK 500 6 ASN A 81 16.72 52.69 REMARK 500 6 LYS A 104 -65.12 -97.08 REMARK 500 7 ARG A 71 -87.41 -90.14 REMARK 500 7 ALA A 72 81.53 -159.24 REMARK 500 7 ASN A 81 13.32 53.24 REMARK 500 7 VAL A 85 -33.54 -133.42 REMARK 500 7 LYS A 104 -61.46 -91.35 REMARK 500 8 ALA A 2 143.24 57.80 REMARK 500 8 ARG A 71 -89.07 -98.58 REMARK 500 8 ALA A 72 82.45 -154.83 REMARK 500 8 ASN A 81 15.35 54.42 REMARK 500 9 ARG A 71 -89.51 -90.85 REMARK 500 9 ALA A 72 84.06 -157.82 REMARK 500 9 ASN A 81 6.14 56.52 REMARK 500 9 LYS A 104 -66.45 -98.73 REMARK 500 10 VAL A 14 -41.46 -132.74 REMARK 500 10 ARG A 71 -86.86 -94.25 REMARK 500 10 ALA A 72 85.51 -157.40 REMARK 500 10 ASN A 81 16.92 51.74 REMARK 500 10 VAL A 85 -37.27 -131.54 REMARK 500 10 LYS A 104 -69.10 -96.02 REMARK 500 11 ARG A 71 -88.35 -91.32 REMARK 500 11 ALA A 72 89.04 -157.01 REMARK 500 11 ASN A 81 3.70 56.93 REMARK 500 12 ARG A 71 -93.86 -93.68 REMARK 500 12 ALA A 72 74.47 -157.96 REMARK 500 12 ASN A 81 17.41 53.79 REMARK 500 13 ARG A 71 -93.03 -94.59 REMARK 500 REMARK 500 THIS ENTRY HAS 79 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 72 ILE A 73 18 -148.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17299 RELATED DB: BMRB REMARK 900 OXIDIZED REMARK 900 RELATED ID: 17300 RELATED DB: BMRB DBREF 6ZOM A 1 107 UNP Q72B01 Q72B01_DESVH 1 107 SEQADV 6ZOM HIS A -5 UNP Q72B01 EXPRESSION TAG SEQADV 6ZOM HIS A -4 UNP Q72B01 EXPRESSION TAG SEQADV 6ZOM HIS A -3 UNP Q72B01 EXPRESSION TAG SEQADV 6ZOM HIS A -2 UNP Q72B01 EXPRESSION TAG SEQADV 6ZOM HIS A -1 UNP Q72B01 EXPRESSION TAG SEQADV 6ZOM HIS A 0 UNP Q72B01 EXPRESSION TAG SEQRES 1 A 113 HIS HIS HIS HIS HIS HIS MET ALA ALA GLN ILE THR ASP SEQRES 2 A 113 ALA THR PHE GLU ALA SER VAL LEU LYS SER ALA ILE PRO SEQRES 3 A 113 VAL LEU ILE ASP PHE TRP ALA PRO TRP CYS GLY PRO CYS SEQRES 4 A 113 ARG ALA MET GLY PRO VAL ILE ASP GLU LEU ALA ALA GLU SEQRES 5 A 113 TYR GLU GLY LYS VAL LEU ILE VAL LYS MET ASN VAL ASP SEQRES 6 A 113 ASP ASN PRO ALA THR PRO SER LYS TYR GLY ILE ARG ALA SEQRES 7 A 113 ILE PRO THR LEU ILE LEU PHE LYS ASN GLY GLU VAL VAL SEQRES 8 A 113 GLU GLN VAL THR GLY ALA VAL SER LYS SER SER ILE LYS SEQRES 9 A 113 ASP MET ILE ALA GLN LYS ALA LEU GLY HELIX 1 AA1 THR A 6 GLU A 11 1 6 HELIX 2 AA2 CYS A 30 ALA A 35 1 6 HELIX 3 AA3 MET A 36 TYR A 47 1 12 HELIX 4 AA4 PRO A 62 TYR A 68 1 7 HELIX 5 AA5 SER A 93 ALA A 105 1 13 SHEET 1 AA1 5 GLN A 4 ILE A 5 0 SHEET 2 AA1 5 LEU A 52 ASN A 57 1 O LYS A 55 N ILE A 5 SHEET 3 AA1 5 VAL A 21 TRP A 26 1 N ASP A 24 O MET A 56 SHEET 4 AA1 5 THR A 75 LYS A 80 -1 O THR A 75 N PHE A 25 SHEET 5 AA1 5 GLU A 83 THR A 89 -1 O VAL A 88 N LEU A 76 SSBOND 1 CYS A 30 CYS A 33 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1