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- PDB-1clf: CLOSTRIDIUM PASTEURIANUM FERREDOXIN -

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Basic information

Entry
Database: PDB / ID: 1clf
TitleCLOSTRIDIUM PASTEURIANUM FERREDOXIN
ComponentsFERREDOXIN
KeywordsELECTRON TRANSFER (IRON-SULFUR PROTEIN)
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / cytoplasm
Similarity search - Function
7Fe ferredoxin / Alpha-Beta Plaits - #20 / 4Fe-4S binding domain / : / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits ...7Fe ferredoxin / Alpha-Beta Plaits - #20 / 4Fe-4S binding domain / : / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesClostridium pasteurianum (bacteria)
MethodSOLUTION NMR
AuthorsBertini, I. / Donaire, A. / Feinberg, B.A. / Luchinat, C. / Piccioli, M. / Yuan, H.
Citation
Journal: Eur.J.Biochem. / Year: 1995
Title: Solution structure of the oxidized 2[4Fe-4S] ferredoxin from Clostridium pasteurianum.
Authors: Bertini, I. / Donaire, A. / Feinberg, B.A. / Luchinat, C. / Piccioli, M. / Yuan, H.
#1: Journal: J.Am.Chem.Soc. / Year: 1994
Title: The Fe4S4 Centers in Ferredoxins Studied Through Proton and Carbon Hyperfine Coupling. Sequence Specific Assignments of Cysteines in Ferredoxins from Clostridium Acidi Urici and Clostridium Pasteurianum
Authors: Bertini, I. / Cappozzi, F. / Luchinat, C. / Piccioli, M. / Vila, A.J.
#2: Journal: Biochemistry / Year: 1994
Title: Comparison of Native and Mutant Proteins Provides a Sequence-Specific Assignment of the Cysteinyl Ligand Proton NMR Resonances in the 2[Fe4S4] Ferredoxin from Clostridium Pasteurianum
Authors: Scrofani, S.D.B. / Brereton, P.S. / Hamer, A.M. / Lavery, M.J. / Mcdowall, S.G. / Vincent, G.A. / Brownlee, R.T.C. / Hoogenraad, N.J. / Sadek, M. / Wedd, A.G.
#3: Journal: Methods Enzymol. / Year: 1972
Title: Preparation and Properties of Clostridial Ferredoxins
Authors: Rabinowitz, J.
History
DepositionJun 21, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2033
Polymers5,5001
Non-polymers7032
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: VAL 53 - GLN 54 MODEL 1 OMEGA = 221.48 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: GLN 54 - GLU 55 MODEL 1 OMEGA = 146.66 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: VAL 53 - GLN 54 MODEL 2 OMEGA = 211.62 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: TYR 2 - LYS 3 MODEL 3 OMEGA = 146.71 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: VAL 53 - GLN 54 MODEL 3 OMEGA = 215.45 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: TYR 2 - LYS 3 MODEL 4 OMEGA = 135.35 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: VAL 53 - GLN 54 MODEL 4 OMEGA = 216.57 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: TYR 2 - LYS 3 MODEL 5 OMEGA = 143.38 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
9: LYS 3 - ILE 4 MODEL 5 OMEGA = 147.43 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
10: GLY 41 - ASN 42 MODEL 5 OMEGA = 212.47 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
11: VAL 53 - GLN 54 MODEL 5 OMEGA = 220.84 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
12: GLN 54 - GLU 55 MODEL 5 OMEGA = 135.31 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
13: TYR 2 - LYS 3 MODEL 6 OMEGA = 144.67 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
14: LYS 3 - ILE 4 MODEL 6 OMEGA = 146.53 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
15: GLY 41 - ASN 42 MODEL 6 OMEGA = 212.28 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
16: VAL 53 - GLN 54 MODEL 6 OMEGA = 235.88 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
17: TYR 2 - LYS 3 MODEL 7 OMEGA = 140.71 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
18: VAL 53 - GLN 54 MODEL 7 OMEGA = 263.66 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
19: TYR 2 - LYS 3 MODEL 8 OMEGA = 141.08 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
20: VAL 53 - GLN 54 MODEL 8 OMEGA = 238.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
21: ALA 1 - TYR 2 MODEL 9 OMEGA = 142.99 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
22: VAL 53 - GLN 54 MODEL 9 OMEGA = 241.31 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
23: TYR 2 - LYS 3 MODEL 10 OMEGA = 145.78 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
24: VAL 53 - GLN 54 MODEL 10 OMEGA = 227.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
25: GLN 54 - GLU 55 MODEL 10 OMEGA = 131.81 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
26: VAL 53 - GLN 54 MODEL 11 OMEGA = 231.51 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
27: TYR 2 - LYS 3 MODEL 12 OMEGA = 149.84 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
28: VAL 53 - GLN 54 MODEL 12 OMEGA = 229.62 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
29: TYR 2 - LYS 3 MODEL 13 OMEGA = 148.48 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
30: VAL 53 - GLN 54 MODEL 13 OMEGA = 226.49 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
31: GLN 54 - GLU 55 MODEL 13 OMEGA = 144.75 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
32: TYR 2 - LYS 3 MODEL 14 OMEGA = 145.89 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
33: LYS 3 - ILE 4 MODEL 14 OMEGA = 148.07 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
34: VAL 53 - GLN 54 MODEL 14 OMEGA = 231.16 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
35: TYR 2 - LYS 3 MODEL 15 OMEGA = 144.88 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
36: VAL 53 - GLN 54 MODEL 15 OMEGA = 246.86 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
37: TYR 2 - LYS 3 MODEL 16 OMEGA = 146.32 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
38: VAL 53 - GLN 54 MODEL 16 OMEGA = 226.46 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
39: GLN 54 - GLU 55 MODEL 16 OMEGA = 144.95 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / -
Representative

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Components

#1: Protein FERREDOXIN


Mass: 5500.159 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Clostridium pasteurianum (bacteria) / Strain: WINOGRADSKY / References: UniProt: P00195
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other

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Processing

NMR software
NameVersionDeveloperClassification
DIANAGUNTERT,BRAUN,WUTHRICHrefinement
Amber4PEARLMAN,CASE,CALDWELL,SIEBEL,SINGH,WEINER,KOLLMANrefinement
NMR ensembleConformers submitted total number: 16

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