HEADER ELECTRON TRANSPORT 12-JUL-07 2QL0 TITLE ZINC-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: 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 20 AUTHOR B.J.GOODFELLOW,S.G.NUNES,B.F.VOLKMAN,J.G.MOURA,A.L.MACEDO,I.C.DUARTE, AUTHOR 2 J.L.MARKLEY,I.MOURA REVDAT 4 22-MAY-24 2QL0 1 REMARK REVDAT 3 16-MAR-22 2QL0 1 REMARK REVDAT 2 24-FEB-09 2QL0 1 VERSN REVDAT 1 08-JUL-08 2QL0 0 JRNL AUTH B.J.GOODFELLOW,S.G.NUNES,B.F.VOLKMAN,J.J.G.MOURA,A.L.MACEDO, JRNL AUTH 2 I.C.DUARTE,J.L.MARKLEY,I.MOURA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.0, CYANA 2.0 REMARK 3 AUTHORS : G NTERT P. (CYANA), G NTERT P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A FINAL TOTAL OF 581 DISTANCE REMARK 3 CONSTRAINTS WERE USED (INTRA 122; SHORT 147; MED 121; LONG 203). REMARK 4 REMARK 4 2QL0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1000043730. 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 ZN-RUBREDOXIN U-15N; 50MM REMARK 210 PHOSPHATE BUFFER; 2MM ZN- 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; 3D_ REMARK 210 15N-SEPARATED_TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2004, XWINNMR 3.5, REMARK 210 SPARKY 3.112 REMARK 210 METHOD USED : AUTOMATED METHODS ALONG WITH REMARK 210 TORSION ANGLE DYNAMICS WERE USED REMARK 210 FOR BACKBONE CHEMICAL SHIFT REMARK 210 ASSIGNMENT AND ITERATIVE NOE REMARK 210 REFINEMENT. 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 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 LEU A 33 158.75 -45.11 REMARK 500 1 VAL A 41 -60.79 -93.50 REMARK 500 1 CYS A 42 -70.33 -109.04 REMARK 500 2 VAL A 8 -50.99 -121.64 REMARK 500 2 ASP A 19 85.38 -160.43 REMARK 500 2 ASN A 22 -66.07 -90.98 REMARK 500 2 SER A 29 156.56 -41.50 REMARK 500 2 ASP A 32 30.50 -96.16 REMARK 500 2 CYS A 42 -74.74 -110.48 REMARK 500 3 ASP A 19 96.46 -164.22 REMARK 500 3 SER A 29 151.58 -44.24 REMARK 500 3 CYS A 42 -70.20 -109.03 REMARK 500 4 VAL A 8 -54.48 -124.75 REMARK 500 4 TYR A 11 171.45 -59.25 REMARK 500 4 ASP A 19 84.74 178.47 REMARK 500 4 ASN A 22 -51.23 -123.03 REMARK 500 4 SER A 29 159.02 -40.02 REMARK 500 4 LEU A 33 157.57 -44.19 REMARK 500 4 VAL A 41 -60.18 -100.59 REMARK 500 4 CYS A 42 -73.79 -111.23 REMARK 500 5 ASP A 19 96.63 -170.86 REMARK 500 5 VAL A 24 95.52 -64.62 REMARK 500 5 LYS A 25 154.32 -42.16 REMARK 500 5 SER A 29 171.08 -49.47 REMARK 500 5 PRO A 34 -168.16 -74.99 REMARK 500 5 ASP A 36 31.52 -94.93 REMARK 500 5 CYS A 42 -74.66 -111.14 REMARK 500 6 VAL A 41 -60.44 -96.87 REMARK 500 6 CYS A 42 -66.89 -108.85 REMARK 500 7 ASP A 19 99.05 -165.95 REMARK 500 7 LYS A 25 155.34 -49.26 REMARK 500 7 LEU A 33 158.81 -43.85 REMARK 500 7 CYS A 42 -71.96 -111.23 REMARK 500 8 ASP A 19 99.86 178.87 REMARK 500 8 SER A 29 157.97 -47.33 REMARK 500 8 LEU A 33 157.73 -49.88 REMARK 500 8 PRO A 34 -163.99 -74.93 REMARK 500 8 CYS A 42 -72.74 -110.88 REMARK 500 9 ASP A 19 99.91 -167.14 REMARK 500 9 PRO A 34 -163.16 -75.09 REMARK 500 9 CYS A 42 -71.82 -109.84 REMARK 500 10 TYR A 13 138.08 -37.61 REMARK 500 10 LEU A 33 154.94 -48.24 REMARK 500 10 PRO A 34 -167.05 -74.98 REMARK 500 10 CYS A 42 -70.83 -108.86 REMARK 500 11 VAL A 41 -61.68 -96.39 REMARK 500 11 CYS A 42 -63.70 -105.76 REMARK 500 11 GLU A 48 -71.80 -91.88 REMARK 500 11 PHE A 49 136.80 -39.37 REMARK 500 12 THR A 7 35.82 -96.90 REMARK 500 REMARK 500 THIS ENTRY HAS 82 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 ZN A 53 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 CYS A 9 SG 93.3 REMARK 620 3 CYS A 39 SG 106.9 98.0 REMARK 620 4 CYS A 42 SG 123.1 115.3 115.6 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 ZN 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 CENTRE. REMARK 900 RELATED ID: 2QKZ RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE NI SUBSTITUTED FORM OF THE SAME PROTEIN. DBREF 2QL0 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 ZN A 53 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 PRO A 45 SER A 47 5 3 SHEET 1 A 3 GLU A 12 TYR A 13 0 SHEET 2 A 3 TYR A 4 CYS A 6 -1 N TYR A 4 O TYR A 13 SHEET 3 A 3 PHE A 49 ALA A 51 -1 O GLU A 50 N VAL A 5 LINK SG CYS A 6 ZN ZN A 53 1555 1555 2.30 LINK SG CYS A 9 ZN ZN A 53 1555 1555 2.47 LINK SG CYS A 39 ZN ZN A 53 1555 1555 2.47 LINK SG CYS A 42 ZN ZN A 53 1555 1555 2.48 SITE 1 AC1 2 CYS A 6 THR A 7 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