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- PDB-1bd6: 7-FE FERREDOXIN FROM BACILLUS SCHLEGELII, NMR, MINIMIZED AVERAGE ... -

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Basic information

Entry
Database: PDB / ID: 1bd6
Title7-FE FERREDOXIN FROM BACILLUS SCHLEGELII, NMR, MINIMIZED AVERAGE STRUCTURE
Components7-FE FERREDOXIN
KeywordsELECTRON TRANSPORT / IRON-SULFUR
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
7Fe ferredoxin / : / Alpha-Beta Plaits - #20 / 4Fe-4S binding 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
FE3-S4 CLUSTER / IRON/SULFUR CLUSTER / Ferredoxin 7Fe
Similarity search - Component
Biological speciesBacillus schlegelii (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAono, S. / Bentrop, D. / Bertini, I. / Donaire, A. / Luchinat, C. / Niikura, Y. / Rosato, A.
Citation
Journal: Biochemistry / Year: 1998
Title: Solution structure of the oxidized Fe7S8 ferredoxin from the thermophilic bacterium Bacillus schlegelii by 1H NMR spectroscopy.
Authors: Aono, S. / Bentrop, D. / Bertini, I. / Donaire, A. / Luchinat, C. / Niikura, Y. / Rosato, A.
#1: Journal: J.Biol.Inorg.Chem. / Year: 1996
Title: 1H NMR Studies of the Fe7S8 Ferredoxin from Bacillus Schlegelii: A Further Attempt to Understand Fe3S4 Clusters
Authors: Aono, S. / Bertini, I. / Cowan, J.A. / Luchinat, C. / Rosato, A. / Viezzoli, M.S.
#2: Journal: Biochem.Biophys.Res.Commun. / Year: 1994
Title: Cloning and Expression of the Gene Encoding the 7Fe Type Ferredoxin from a Thermophilic Hydrogen Oxidizing Bacterium, Bacillus Schlegelii
Authors: Aono, S. / Nakamura, S. / Aono, R. / Okura, I.
#3: Journal: J.Biochem.(Tokyo) / Year: 1992
Title: Purification and Characterization of a 7Fe Ferredoxin from a Thermophilic Hydrogen-Oxidizing Bacterium, Bacillus Schlegelii
Authors: Aono, S. / Kurita, H. / Uno, S. / Okura, I.
History
DepositionMay 6, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: 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_conn_angle / pdbx_struct_oper_list / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: 7-FE FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3983
Polymers8,7511
Non-polymers6472
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 300
Representative

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Components

#1: Protein 7-FE FERREDOXIN


Mass: 8750.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus schlegelii (bacteria) / Plasmid: PKKFD54 / Production host: Escherichia coli (E. coli) / Strain (production host): JM 109 / References: UniProt: Q45560
#2: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX600BrukerAMX6005001
Bruker DRX 500BrukerDRX 5006002

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Processing

Software
NameClassification
DYANAmodel building
AMBERrefinement
DYANArefinement
NMR software
NameVersionDeveloperClassification
Amber4.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
DYANAstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: THE STRUCTURE CALCULATIONS WERE CARRIED OUT WITH THE PROGRAM DYANA (BY GUNTERT,MUMENTHALER,WUTHRICH). THE 20 STRUCTURES OF THE DYANA FAMILY WITH THE LOWEST TARGET FUNCTION VALUES WERE ...Details: THE STRUCTURE CALCULATIONS WERE CARRIED OUT WITH THE PROGRAM DYANA (BY GUNTERT,MUMENTHALER,WUTHRICH). THE 20 STRUCTURES OF THE DYANA FAMILY WITH THE LOWEST TARGET FUNCTION VALUES WERE REFINED BY RESTRAINED ENERGY MINIMIZATION (REM) AND RESTRAINED MOLECULAR DYNAMICS (RMD) IN VACUO. THE STRUCTURE IN THIS ENTRY REPRESENTS THE MINIMIZED AVERAGE STRUCTURE OF THE RMD FAMILY. REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformers calculated total number: 300 / Conformers submitted total number: 1

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