HEADER OXIDOREDUCTASE 29-AUG-05 2AUV TITLE SOLUTION STRUCTURE OF HNDAC : A THIOREDOXIN-LIKE [2FE-2S] FERREDOXIN TITLE 2 INVOLVED IN THE NADP-REDUCING HYDROGENASE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: POTENTIAL NAD-REDUCING HYDROGENASE SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SUBUNIT A C-TERMINAL DOMAIN; COMPND 5 EC: 1.12.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO FRUCTOSOVORANS; SOURCE 3 ORGANISM_TAXID: 878; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-HNDAC KEYWDS THIOREDOXIN, THIORDOXIN-LIKE, OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR M.NOUAILLER,X.MORELLI,O.BORNET,B.CHETRIT,Z.DERMOUN,F.GUERLESQUIN REVDAT 3 09-MAR-22 2AUV 1 REMARK LINK REVDAT 2 24-FEB-09 2AUV 1 VERSN REVDAT 1 27-JUN-06 2AUV 0 JRNL AUTH M.NOUAILLER,X.MORELLI,O.BORNET,B.CHETRIT,Z.DERMOUN, JRNL AUTH 2 F.GUERLESQUIN JRNL TITL SOLUTION STRUCTURE OF HNDAC: A THIOREDOXIN-LIKE DOMAIN JRNL TITL 2 INVOLVED IN THE NADP-REDUCING HYDROGENASE COMPLEX JRNL REF PROTEIN SCI. V. 15 1369 2006 JRNL REFN ISSN 0961-8368 JRNL PMID 16731971 JRNL DOI 10.1110/PS.051916606 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.0, ARIA 1.2 REMARK 3 AUTHORS : BRUKER (XWINNMR), JP LINGE, SI O'DONOGHUE AND M REMARK 3 NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AUV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000034340. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 10MM SODIUM PHOSPHATE BUFFER, REMARK 210 100MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM OXIDIZED HNDAC, 10MM SODIUM REMARK 210 PHOSPHATE BUFFER (PH 6.0), 100MM REMARK 210 NACL; 1MM OXIDIZED HNDAC; 1MM REMARK 210 OXIDIZED HNDAC U-15N, 10MM REMARK 210 SODIUM PHOSPHATE BUFFER (PH 6.0), REMARK 210 100MM NACL; 0.15MM OXIDIZED REMARK 210 HNDAC U-15N,13C, 10MM SODIUM REMARK 210 PHOSPHATE BUFFER (PH 6.0), 100MM REMARK 210 NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; REMARK 210 3D_15N-SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_TOCSY; HNCA-J REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.0, FELIX 2002, CNS REMARK 210 1.1, ARIA 1.2 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES AND 2D/3D HETERONUCLEAR TECHNIQUES 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HA2 GLY A 5 HB2 SER A 47 1.16 REMARK 500 OD2 ASP A 39 H PHE A 46 1.58 REMARK 500 O LEU A 33 H ILE A 35 1.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 3 TYR A 70 CE1 TYR A 70 CZ -0.086 REMARK 500 5 TYR A 7 CE1 TYR A 7 CZ -0.089 REMARK 500 5 TYR A 7 CZ TYR A 7 CE2 0.132 REMARK 500 10 TYR A 7 CZ TYR A 7 CE2 0.102 REMARK 500 12 TYR A 7 CE1 TYR A 7 CZ -0.104 REMARK 500 12 TYR A 7 CZ TYR A 7 CE2 0.107 REMARK 500 14 TYR A 70 CE1 TYR A 70 CZ 0.102 REMARK 500 14 TYR A 70 CZ TYR A 70 CE2 -0.103 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 PRO A 8 94.35 -52.72 REMARK 500 1 LYS A 34 -18.81 61.04 REMARK 500 1 ILE A 35 -164.50 51.71 REMARK 500 1 ASP A 36 -55.64 -155.51 REMARK 500 1 ILE A 37 9.98 -167.53 REMARK 500 1 VAL A 40 -68.33 18.83 REMARK 500 1 PRO A 42 89.56 -33.06 REMARK 500 1 ASP A 43 -65.10 -144.36 REMARK 500 1 CYS A 57 -33.32 -133.19 REMARK 500 1 GLU A 67 25.88 -79.53 REMARK 500 1 VAL A 69 99.53 46.26 REMARK 500 1 TYR A 70 -153.21 -117.03 REMARK 500 1 VAL A 73 -90.31 -126.41 REMARK 500 1 THR A 74 -66.60 -137.77 REMARK 500 2 PRO A 8 92.81 -61.48 REMARK 500 2 LYS A 34 -19.52 65.77 REMARK 500 2 ILE A 35 -170.17 54.36 REMARK 500 2 ASP A 36 -49.56 -157.38 REMARK 500 2 ILE A 37 5.87 -164.92 REMARK 500 2 VAL A 40 -71.73 54.99 REMARK 500 2 THR A 41 -57.72 -151.18 REMARK 500 2 ARG A 45 -64.69 -94.70 REMARK 500 2 CYS A 57 -32.65 -135.70 REMARK 500 2 GLU A 67 37.96 -78.83 REMARK 500 2 VAL A 69 113.72 47.54 REMARK 500 2 VAL A 73 -165.05 64.33 REMARK 500 2 THR A 74 -46.67 -138.58 REMARK 500 3 LYS A 4 -74.38 -50.37 REMARK 500 3 PRO A 8 96.55 -53.34 REMARK 500 3 LYS A 34 -21.86 70.16 REMARK 500 3 ILE A 35 -176.47 56.56 REMARK 500 3 ASP A 36 -44.11 -158.68 REMARK 500 3 ILE A 37 -0.94 -168.30 REMARK 500 3 ASP A 39 135.54 -171.54 REMARK 500 3 VAL A 40 -65.57 39.06 REMARK 500 3 THR A 41 -60.11 -150.82 REMARK 500 3 ASP A 43 -1.75 83.38 REMARK 500 3 CYS A 57 -32.49 -135.12 REMARK 500 3 GLU A 67 34.48 -79.06 REMARK 500 3 VAL A 69 108.10 36.54 REMARK 500 3 VAL A 73 -168.56 63.31 REMARK 500 3 THR A 74 -46.36 -135.74 REMARK 500 4 PRO A 8 96.78 -50.69 REMARK 500 4 LYS A 34 -27.34 68.09 REMARK 500 4 ILE A 35 -173.89 55.55 REMARK 500 4 ASP A 36 -53.55 -155.14 REMARK 500 4 ILE A 37 19.42 -174.43 REMARK 500 4 ASP A 39 119.82 -165.27 REMARK 500 4 VAL A 40 -65.40 56.11 REMARK 500 4 THR A 41 -59.79 -164.19 REMARK 500 REMARK 500 THIS ENTRY HAS 235 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 THR A 41 PRO A 42 1 -149.01 REMARK 500 THR A 50 LEU A 51 1 -149.84 REMARK 500 THR A 50 LEU A 51 3 -147.97 REMARK 500 THR A 50 LEU A 51 4 -147.84 REMARK 500 ILE A 62 VAL A 63 6 147.56 REMARK 500 THR A 50 LEU A 51 8 -148.02 REMARK 500 THR A 50 LEU A 51 10 -148.17 REMARK 500 THR A 50 LEU A 51 11 -149.25 REMARK 500 ASN A 72 VAL A 73 11 -148.58 REMARK 500 ILE A 62 VAL A 63 14 148.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 5 TYR A 7 0.08 SIDE CHAIN REMARK 500 6 TYR A 7 0.08 SIDE CHAIN REMARK 500 10 TYR A 7 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 86 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 17 SG REMARK 620 2 FES A 86 S1 111.4 REMARK 620 3 FES A 86 S2 145.1 94.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 86 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 57 SG REMARK 620 2 FES A 86 S1 128.0 REMARK 620 3 FES A 86 S2 113.3 69.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES A 86 DBREF 2AUV A 1 85 UNP Q46505 Q46505_DESFR 87 171 SEQRES 1 A 85 MET VAL PRO LYS GLY LYS TYR PRO ILE SER VAL CYS MET SEQRES 2 A 85 GLY THR ALA CYS PHE VAL LYS GLY ALA ASP LYS VAL VAL SEQRES 3 A 85 HIS ALA PHE LYS GLU GLN LEU LYS ILE ASP ILE GLY ASP SEQRES 4 A 85 VAL THR PRO ASP GLY ARG PHE SER ILE ASP THR LEU ARG SEQRES 5 A 85 CYS VAL GLY GLY CYS ALA LEU ALA PRO ILE VAL MET VAL SEQRES 6 A 85 GLY GLU LYS VAL TYR GLY ASN VAL THR PRO GLY GLN VAL SEQRES 7 A 85 LYS LYS ILE LEU ALA GLU TYR HET FES A 86 4 HETNAM FES FE2/S2 (INORGANIC) CLUSTER FORMUL 2 FES FE2 S2 HELIX 1 1 GLY A 14 VAL A 19 1 6 HELIX 2 2 GLY A 21 LYS A 34 1 14 HELIX 3 3 GLU A 67 VAL A 69 5 3 HELIX 4 4 GLY A 76 TYR A 85 1 10 SHEET 1 A 2 ILE A 9 SER A 10 0 SHEET 2 A 2 MET A 64 VAL A 65 -1 O MET A 64 N SER A 10 LINK SG CYS A 17 FE1 FES A 86 1555 1555 2.23 LINK SG CYS A 57 FE2 FES A 86 1555 1555 2.25 SITE 1 AC1 6 CYS A 12 CYS A 17 CYS A 53 VAL A 54 SITE 2 AC1 6 GLY A 55 CYS A 57 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