HEADER ELECTRON TRANSPORT 12-JUL-07 2QKZ OBSLTE 26-JAN-10 2QKZ 2KKD TITLE NICKEL-SUBSTITUTED RUBREDOXIN FROM DESULFOVIBRIO VULGARIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBREDOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RD; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS; SOURCE 3 STRAIN: HILDENBOROUGH/ATCC 29579/NCIMB 8303; SOURCE 4 GENE: RUB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI KEYWDS [FE-4S], ELECTRON TRANSPORT, IRON, METAL-BINDING EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR B.J.GOODFELLOW,S.G.NUNES,B.F.VOLKMAN,J.J.G.MOURA,A.L.MACEDO, AUTHOR 2 I.C.DUARTE,J.L.MARKLEY,I.MOURA REVDAT 3 26-JAN-10 2QKZ 1 OBSLTE REVDAT 2 24-FEB-09 2QKZ 1 VERSN REVDAT 1 08-JUL-08 2QKZ 0 JRNL AUTH B.J.GOODFELLOW,S.G.NUNES,B.F.VOLKMAN,J.J.G.MOURA, JRNL AUTH 2 A.L.MACEDO,I.C.DUARTE,J.L.MARKLEY,I.MOURA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PSEUDYANA 1.5 REMARK 3 AUTHORS : BANCI L, BERTINI I, CREMONINI MA, GORI- REMARK 3 SAVELLINI G, LUCHINAT C, WURTHRICH K, GUNTERT PG REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 A TOTAL OF 529 CONSTRAINTS (161 INTRA, 95 SHORT, 96 MEDIUM, 177 REMARK 3 LONG). HYDROGEN BONDS DISTANCE CONSTRAINTS: 16. REMARK 3 A TOTAL OF 147 PSEUDOCONTACT SHIFTS RESTRAINTS WERE ALSO USED REMARK 3 FOR STRUCTURE REFINEMENT. REMARK 4 REMARK 4 2QKZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-07. REMARK 100 THE RCSB ID CODE IS RCSB043729. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM NI-RUBREDOXIN U-15N; 50MM REMARK 210 PHOSPHATE BUFFER; 2MM NI- REMARK 210 RUBREDOXIN UNLABELED; 50MM REMARK 210 PHOSPHATE BUFFER; 2MM NI- REMARK 210 RUBREDOXIN UNLABELED; 50MM REMARK 210 PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 2D REMARK 210 NOESY; 2D TOCSY; 15N-1H HSQC; REMARK 210 3D_15N-SEPARATED_TOCSY; 1D NOE REMARK 210 DIFFERENCE WITH SUPER-WEFT; 2D REMARK 210 NOESY WITH FAST RECYCLE REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 750 MHZ; 600 MHZ; REMARK 210 400 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, NMRPIPE 2004, REMARK 210 XWINNMR 3.5, SPARKY 3.112, REMARK 210 FANTASIAN 2.0, PSEUDYANA 1.5 REMARK 210 METHOD USED : AUTOMATED METHODS ALONG WITH REMARK 210 TORSION ANGLE DYNAMICS WERE REMARK 210 USED FOR BACKBONE CHEMICAL REMARK 210 SHIFT ASSIGNMENT AND ITERATIVE REMARK 210 NOE REFINEMENT. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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 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 O PRO A 45 H GLU A 48 1.45 REMARK 500 O ASP A 19 H VAL A 24 1.53 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 TYR A 4 -165.02 -107.39 REMARK 500 1 THR A 7 38.28 -86.77 REMARK 500 1 VAL A 8 11.30 -140.40 REMARK 500 1 CYS A 9 -38.67 179.55 REMARK 500 1 TYR A 11 -166.81 -78.15 REMARK 500 1 ASP A 19 109.52 178.68 REMARK 500 1 ASP A 21 -36.68 -38.21 REMARK 500 1 CYS A 39 114.69 -36.69 REMARK 500 1 VAL A 41 -45.86 -160.97 REMARK 500 2 LYS A 2 -133.82 42.87 REMARK 500 2 LYS A 3 119.65 64.80 REMARK 500 2 TYR A 4 -161.63 -113.77 REMARK 500 2 THR A 7 -31.70 -37.44 REMARK 500 2 CYS A 9 -52.22 82.60 REMARK 500 2 GLU A 17 -58.39 -123.16 REMARK 500 2 ASP A 19 118.23 175.79 REMARK 500 2 VAL A 38 -127.89 41.62 REMARK 500 2 VAL A 41 -53.23 -122.53 REMARK 500 2 CYS A 42 -159.87 -97.16 REMARK 500 2 ALA A 44 130.98 -36.80 REMARK 500 3 LYS A 2 -161.85 -161.20 REMARK 500 3 LYS A 3 124.06 66.85 REMARK 500 3 TYR A 4 -164.70 -111.05 REMARK 500 3 VAL A 8 -55.75 -156.10 REMARK 500 3 ASP A 19 106.50 -179.55 REMARK 500 3 ASP A 21 -37.09 -38.27 REMARK 500 3 ASN A 22 -63.27 -105.12 REMARK 500 3 VAL A 38 -124.05 44.36 REMARK 500 3 ALA A 44 126.11 -30.60 REMARK 500 4 LYS A 2 -148.95 64.69 REMARK 500 4 LYS A 3 94.76 42.47 REMARK 500 4 TYR A 4 -166.13 -79.51 REMARK 500 4 THR A 7 23.33 48.12 REMARK 500 4 VAL A 8 -58.53 -144.81 REMARK 500 4 GLU A 17 -60.77 -123.24 REMARK 500 4 ASP A 19 106.50 177.74 REMARK 500 4 VAL A 38 -128.94 44.70 REMARK 500 4 CYS A 42 -165.31 -108.30 REMARK 500 4 ALA A 44 128.38 -32.16 REMARK 500 5 LYS A 2 144.06 173.76 REMARK 500 5 THR A 7 46.41 -97.32 REMARK 500 5 VAL A 8 -45.52 -149.54 REMARK 500 5 ASP A 19 107.33 179.61 REMARK 500 5 ASP A 21 -38.73 -38.29 REMARK 500 5 VAL A 38 -137.83 44.72 REMARK 500 5 VAL A 41 20.86 -145.77 REMARK 500 5 ALA A 44 117.92 -23.83 REMARK 500 6 LYS A 2 153.38 60.33 REMARK 500 6 LYS A 3 94.48 47.13 REMARK 500 6 TYR A 4 -163.36 -116.95 REMARK 500 REMARK 500 THIS ENTRY HAS 136 RAMACHANDRAN OUTLIERS. 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 1 NI A 53 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 CYS A 9 SG 103.8 REMARK 620 3 CYS A 39 SG 95.3 125.2 REMARK 620 4 CYS A 42 SG 83.8 110.3 122.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 53 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8RXN RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE SAME PROTEIN, BUT WITH NATIVE IRON REMARK 900 CENTRE. REMARK 900 RELATED ID: 2QL0 RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE ZN SUBSTITUTED FORM OF THE SAME REMARK 900 PROTEIN. DBREF 2QKZ A 1 52 UNP P00269 RUBR_DESVH 1 52 SEQRES 1 A 52 MET LYS LYS TYR VAL CYS THR VAL CYS GLY TYR GLU TYR SEQRES 2 A 52 ASP PRO ALA GLU GLY ASP PRO ASP ASN GLY VAL LYS PRO SEQRES 3 A 52 GLY THR SER PHE ASP ASP LEU PRO ALA ASP TRP VAL CYS SEQRES 4 A 52 PRO VAL CYS GLY ALA PRO LYS SER GLU PHE GLU ALA ALA HET NI A 53 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI NI 2+ HELIX 1 1 SER A 29 LEU A 33 5 5 HELIX 2 2 PRO A 45 SER A 47 5 3 SHEET 1 A 2 VAL A 5 CYS A 6 0 SHEET 2 A 2 PHE A 49 GLU A 50 -1 O GLU A 50 N VAL A 5 LINK SG CYS A 6 NI NI A 53 1555 1555 2.44 LINK SG CYS A 9 NI NI A 53 1555 1555 2.63 LINK SG CYS A 39 NI NI A 53 1555 1555 2.02 LINK SG CYS A 42 NI NI A 53 1555 1555 2.60 SITE 1 AC1 3 CYS A 6 CYS A 9 TYR A 11 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