PDB Short entry for 2KKD HEADER ELECTRON TRANSPORT 18-JUN-09 2KKD TITLE NMR STRUCTURE OF NI SUBSTITUED DESULFOVIBRIO VULGARIS RUBREDOXIN 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 STR. HILDENBOROUGH; SOURCE 3 ORGANISM_TAXID: 882; SOURCE 4 STRAIN: HIDENBOROUGH/ATCC 29579/NCIMB 8303; SOURCE 5 GENE: RUB, DVU_3184; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PT7-7 KEYWDS ELECTRON TRANSPORT, [FE-4S], IRON, METAL-BINDING, CYTOPLASM, KEYWDS 2 TRANSPORT EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR S.G.NUNES,B.F.VOLKMAN,J.J.G.MOURA,I.MOURA,A.L.MACEDO,J.L.MARKLEY, AUTHOR 2 I.C.DUARTE REVDAT 4 16-MAR-22 2KKD 1 REMARK LINK REVDAT 3 16-MAR-10 2KKD 1 JRNL REVDAT 2 26-JAN-10 2KKD 1 SPRSDE REVDAT 1 22-DEC-09 2KKD 0 SPRSDE 26-JAN-10 2KKD 2QKZ JRNL AUTH B.J.GOODFELLOW,I.C.DUARTE,A.L.MACEDO,B.F.VOLKMAN,S.G.NUNES, JRNL AUTH 2 I.MOURA,J.L.MARKLEY,J.J.MOURA JRNL TITL AN NMR STRUCTURAL STUDY OF NICKEL-SUBSTITUTED RUBREDOXIN JRNL REF J.BIOL.INORG.CHEM. V. 15 409 2010 JRNL REFN ISSN 0949-8257 JRNL PMID 19997764 JRNL DOI 10.1007/S00775-009-0613-6 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA REMARK 3 AUTHORS : GUNTERT P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE REFINEMENT USED PSEUDOCONTACT REMARK 3 SHIFTS REMARK 4 REMARK 4 2KKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000101228. 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 : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 50 MM SODIUM PHOSPHATE-1, 90% REMARK 210 H2O/10% D2O; 50 MM SODIUM REMARK 210 PHOSPHATE-2, 90% H2O/10% D2O; 2 REMARK 210 MM SODIUM AZIDE-3, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-15N REMARK 210 TOCSY; 2D 1H-15N HSQC; 2D 1H-1H REMARK 210 NOESY; 2D 1H-1H TOCSY; 2D NOESY REMARK 210 WITH FAST RECYCLE; 1D NOE REMARK 210 DIFFERENCE WITH SUPER-WEFT REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 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 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 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 LYS A 3 108.44 -40.62 REMARK 500 1 THR A 7 43.06 -104.82 REMARK 500 1 VAL A 8 -45.50 -148.18 REMARK 500 1 CYS A 9 -50.87 -122.35 REMARK 500 1 ASP A 19 108.70 -174.15 REMARK 500 1 LEU A 33 157.33 -47.51 REMARK 500 1 CYS A 39 103.23 -43.26 REMARK 500 1 VAL A 41 -45.24 -145.79 REMARK 500 1 ALA A 44 142.34 -25.86 REMARK 500 2 LYS A 2 -168.30 84.39 REMARK 500 2 LYS A 3 115.77 63.31 REMARK 500 2 THR A 7 36.85 71.30 REMARK 500 2 VAL A 8 -45.38 -152.56 REMARK 500 2 CYS A 39 104.87 -38.54 REMARK 500 2 PRO A 40 44.67 -74.98 REMARK 500 2 VAL A 41 -57.87 -136.48 REMARK 500 3 THR A 7 29.63 80.10 REMARK 500 3 VAL A 8 -44.81 -146.35 REMARK 500 3 TYR A 11 111.04 -162.65 REMARK 500 3 ASP A 19 121.91 -179.95 REMARK 500 3 LEU A 33 153.36 -46.55 REMARK 500 3 CYS A 39 104.37 -38.75 REMARK 500 3 PRO A 40 42.52 -75.05 REMARK 500 3 VAL A 41 -53.61 -133.42 REMARK 500 4 LYS A 2 -149.03 87.25 REMARK 500 4 LYS A 3 117.69 63.30 REMARK 500 4 THR A 7 40.63 -94.37 REMARK 500 4 VAL A 8 -43.18 -145.44 REMARK 500 4 CYS A 9 -50.42 -128.24 REMARK 500 4 TYR A 11 92.26 35.22 REMARK 500 4 ASP A 19 108.98 -176.08 REMARK 500 4 LEU A 33 150.27 -39.76 REMARK 500 4 CYS A 39 104.19 -40.95 REMARK 500 4 PRO A 40 49.45 -75.05 REMARK 500 4 VAL A 41 -59.11 -144.22 REMARK 500 5 LYS A 2 -169.78 -77.11 REMARK 500 5 LYS A 3 116.25 68.83 REMARK 500 5 VAL A 8 -45.59 -143.30 REMARK 500 5 CYS A 9 -50.08 -123.40 REMARK 500 5 TYR A 11 104.69 -169.63 REMARK 500 5 ASP A 19 121.00 179.58 REMARK 500 5 CYS A 39 104.94 -37.34 REMARK 500 5 PRO A 40 46.52 -75.01 REMARK 500 5 VAL A 41 -52.63 -138.62 REMARK 500 6 LYS A 3 121.00 69.45 REMARK 500 6 VAL A 8 -83.40 -65.00 REMARK 500 6 GLU A 12 118.51 -35.61 REMARK 500 6 ASP A 19 108.85 -176.90 REMARK 500 6 CYS A 39 104.76 -39.95 REMARK 500 6 VAL A 41 -52.26 -147.24 REMARK 500 REMARK 500 THIS ENTRY HAS 123 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 NI A 53 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 CYS A 9 SG 112.8 REMARK 620 3 CYS A 39 SG 111.4 94.4 REMARK 620 4 CYS A 42 SG 111.3 113.3 112.6 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 STUCTURE OF SAME PROTEIN BUT WITH NATIVE FE CENTRE REMARK 900 RELATED ID: 2QL0 RELATED DB: PDB REMARK 900 NMR STUCTURE OF THE ZN SUBSTITUTED FORM OF THE SAME PROTEIN DBREF 2KKD 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 2.42 LINK SG CYS A 9 NI NI A 53 1555 1555 2.40 LINK SG CYS A 39 NI NI A 53 1555 1555 2.41 LINK SG CYS A 42 NI NI A 53 1555 1555 2.40 SITE 1 AC1 5 CYS A 6 CYS A 9 CYS A 39 CYS A 42 SITE 2 AC1 5 ALA A 44 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