PDB Short entry for 2N5A HEADER OXIDOREDUCTASE 13-JUL-15 2N5A TITLE STRUCTURES OF THE REDUCED STATE OF THE MUTANT D24A OF YEAST TITLE 2 THIOREDOXIN 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: THIOREDOXIN I, TR-I, THIOREDOXIN-2; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: TRX1, TRX2, YLR043C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET17B KEYWDS REDOX CATALYTIC ACTIVITY, WATER CAVITY, PROTEIN HYDRATION, KEYWDS 2 OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.IQBAL,A.H.MORAES,A.P.VALENTE,F.C.L.ALMEIDA REVDAT 2 02-MAR-16 2N5A 1 JRNL REVDAT 1 28-OCT-15 2N5A 0 JRNL AUTH A.IQBAL,A.H.MORAES,A.P.VALENTE,F.C.ALMEIDA JRNL TITL STRUCTURES OF THE REDUCED AND OXIDIZED STATE OF THE MUTANT JRNL TITL 2 D24A OF YEAST THIOREDOXIN 1: INSIGHTS INTO THE MECHANISM FOR JRNL TITL 3 THE CLOSING OF THE WATER CAVITY. JRNL REF J.BIOMOL.NMR V. 63 417 2015 JRNL REFN ISSN 0925-2738 JRNL PMID 26482062 JRNL DOI 10.1007/S10858-015-9996-6 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3, CNS REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), BRUNGER, REMARK 3 ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUL-15. REMARK 100 THE RCSB ID CODE IS RCSB104439. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.02 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 850 UM [U-100% 13C; U-100% 15N] REMARK 210 YTRX1D24A REDUCED, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C HSQC AROMATIC; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D HNCACB; REMARK 210 3D HCCH-TOCSY; 3D HCCH-COSY; 3D REMARK 210 HBHA(CO)NH; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 2.3, CNS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: TORSION ANGLE SIMULATED ANNEALING 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 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 1 ASP A 18 40.46 -81.33 REMARK 500 1 GLU A 68 26.68 80.17 REMARK 500 1 VAL A 84 -28.14 -150.59 REMARK 500 2 ASP A 18 48.16 -80.32 REMARK 500 2 PRO A 32 3.28 -67.35 REMARK 500 2 GLU A 68 27.28 80.28 REMARK 500 2 VAL A 84 -34.34 -151.51 REMARK 500 2 VAL A 88 55.85 -90.09 REMARK 500 2 PRO A 92 -84.12 -25.13 REMARK 500 3 ASP A 18 36.47 -83.62 REMARK 500 3 PRO A 32 8.86 -67.55 REMARK 500 3 LEU A 60 76.45 -111.90 REMARK 500 3 GLU A 68 22.27 80.46 REMARK 500 3 VAL A 84 -24.50 -152.68 REMARK 500 4 ASP A 18 34.43 -79.56 REMARK 500 4 PRO A 32 25.66 -77.91 REMARK 500 4 VAL A 84 -28.27 -151.03 REMARK 500 4 VAL A 88 50.72 -99.94 REMARK 500 4 PRO A 92 -83.70 -21.93 REMARK 500 5 ASP A 18 39.34 -87.99 REMARK 500 5 PRO A 32 20.85 -75.25 REMARK 500 5 GLU A 68 25.85 80.69 REMARK 500 5 VAL A 84 -35.57 -148.84 REMARK 500 5 VAL A 88 52.04 -103.90 REMARK 500 6 ASP A 18 44.93 -83.53 REMARK 500 6 PRO A 32 3.59 -61.33 REMARK 500 6 PRO A 48 2.37 -68.44 REMARK 500 6 VAL A 84 -33.56 -153.86 REMARK 500 6 VAL A 88 48.31 -101.69 REMARK 500 6 PRO A 92 -67.20 -28.53 REMARK 500 7 ASP A 18 40.68 -79.73 REMARK 500 7 PRO A 48 2.04 -68.28 REMARK 500 7 GLU A 83 -178.36 -66.57 REMARK 500 7 VAL A 84 -31.68 -151.12 REMARK 500 7 VAL A 88 43.15 -109.23 REMARK 500 7 ALA A 90 109.59 -59.63 REMARK 500 7 PRO A 92 -79.35 -26.26 REMARK 500 8 PRO A 32 5.08 -67.11 REMARK 500 8 LEU A 60 71.81 -116.04 REMARK 500 8 GLU A 68 19.49 80.99 REMARK 500 8 VAL A 84 -34.42 -149.23 REMARK 500 8 VAL A 88 52.13 -92.09 REMARK 500 8 PRO A 92 -75.78 -21.37 REMARK 500 9 ASP A 18 32.23 -80.78 REMARK 500 9 PRO A 32 12.80 -69.21 REMARK 500 9 LEU A 60 73.65 -105.33 REMARK 500 9 GLU A 68 19.88 80.08 REMARK 500 9 VAL A 84 -28.16 -149.11 REMARK 500 9 VAL A 88 52.60 -99.80 REMARK 500 10 ASP A 18 36.90 -82.52 REMARK 500 REMARK 500 THIS ENTRY HAS 109 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2I9H RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF THE REDUCED FORM OF THIOREDOXIN 1 REMARK 900 FROM SACHAROMYCES CEREVISIAE REMARK 900 RELATED ID: 25702 RELATED DB: BMRB REMARK 900 RELATED ID: 2N5B RELATED DB: PDB DBREF 2N5A A 1 103 UNP P22217 TRX1_YEAST 1 103 SEQADV 2N5A ALA A 24 UNP P22217 ASP 24 ENGINEERED MUTATION SEQRES 1 A 103 MET VAL THR GLN PHE LYS THR ALA SER GLU PHE ASP SER SEQRES 2 A 103 ALA ILE ALA GLN ASP LYS LEU VAL VAL VAL ALA PHE TYR SEQRES 3 A 103 ALA THR TRP CYS GLY PRO CYS LYS MET ILE ALA PRO MET SEQRES 4 A 103 ILE GLU LYS PHE SER GLU GLN TYR PRO GLN ALA ASP PHE SEQRES 5 A 103 TYR LYS LEU ASP VAL ASP GLU LEU GLY ASP VAL ALA GLN SEQRES 6 A 103 LYS ASN GLU VAL SER ALA MET PRO THR LEU LEU LEU PHE SEQRES 7 A 103 LYS ASN GLY LYS GLU VAL ALA LYS VAL VAL GLY ALA ASN SEQRES 8 A 103 PRO ALA ALA ILE LYS GLN ALA ILE ALA ALA ASN ALA HELIX 1 1 THR A 7 ALA A 16 1 10 HELIX 2 2 PRO A 32 TYR A 47 1 16 HELIX 3 3 LEU A 60 GLU A 68 1 9 HELIX 4 4 ASN A 91 ALA A 103 1 13 SHEET 1 A 5 THR A 3 GLN A 4 0 SHEET 2 A 5 ASP A 51 ASP A 56 1 O LYS A 54 N THR A 3 SHEET 3 A 5 VAL A 21 TYR A 26 1 N ALA A 24 O TYR A 53 SHEET 4 A 5 THR A 74 LYS A 79 -1 O THR A 74 N PHE A 25 SHEET 5 A 5 LYS A 82 VAL A 87 -1 O LYS A 82 N LYS A 79 CISPEP 1 MET A 72 PRO A 73 1 -2.07 CISPEP 2 MET A 72 PRO A 73 2 -1.77 CISPEP 3 MET A 72 PRO A 73 3 -9.74 CISPEP 4 MET A 72 PRO A 73 4 -3.95 CISPEP 5 MET A 72 PRO A 73 5 -3.64 CISPEP 6 MET A 72 PRO A 73 6 -2.75 CISPEP 7 MET A 72 PRO A 73 7 -4.56 CISPEP 8 MET A 72 PRO A 73 8 -0.76 CISPEP 9 MET A 72 PRO A 73 9 -5.15 CISPEP 10 MET A 72 PRO A 73 10 -2.08 CISPEP 11 MET A 72 PRO A 73 11 -3.63 CISPEP 12 MET A 72 PRO A 73 12 -0.69 CISPEP 13 MET A 72 PRO A 73 13 -1.99 CISPEP 14 MET A 72 PRO A 73 14 -1.11 CISPEP 15 MET A 72 PRO A 73 15 -3.36 CISPEP 16 MET A 72 PRO A 73 16 -3.13 CISPEP 17 MET A 72 PRO A 73 17 -0.32 CISPEP 18 MET A 72 PRO A 73 18 -4.77 CISPEP 19 MET A 72 PRO A 73 19 -3.13 CISPEP 20 MET A 72 PRO A 73 20 -4.25 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