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- PDB-1bwe: ARTIFICIAL FE8S8 FERREDOXIN: THE D13C VARIANT OF BACILLUS SCHLEGE... -

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Basic information

Entry
Database: PDB / ID: 1bwe
TitleARTIFICIAL FE8S8 FERREDOXIN: THE D13C VARIANT OF BACILLUS SCHLEGELII FE7S8 FERREDOXIN
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT / IRON-SULFUR PROTEIN
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 / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / 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 7Fe
Similarity search - Component
Biological speciesBacillus schlegelii (bacteria)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, RESTRAINED ENERGY MINIMIZATION, RESTRAINED MOLECULAR DYNAMICS
AuthorsAono, S. / Bentrop, D. / Bertini, I. / Cosenza, G. / Luchinat, C.
Citation
Journal: Eur.J.Biochem. / Year: 1998
Title: Solution structure of an artificial Fe8S8 ferredoxin: the D13C variant of Bacillus schlegelii Fe7S8 ferredoxin.
Authors: Aono, S. / Bentrop, D. / Bertini, I. / Cosenza, G. / Luchinat, C.
#1: Journal: FEBS Lett. / Year: 1997
Title: The D13C Variant of Bacillus Schlegelii 7Fe Ferredoxin is an 8Fe Ferredoxin as Revealed by 1H-NMR Spectroscopy
Authors: Aono, S. / Bentrop, D. / Bertini, I. / Luchinat, C. / Macinai, R.
History
DepositionSep 23, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 30, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 6, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_struct_assembly ...atom_site / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_struct_conn_angle.value
Revision 2.1Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_nmr_ensemble / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_software.version / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)9,4423
Polymers8,7391
Non-polymers7032
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the least restraint violations
Representative

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Components

#1: Protein FERREDOXIN /


Mass: 8738.883 Da / Num. of mol.: 1 / Mutation: D13C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus schlegelii (bacteria) / Plasmid: PKKFD D13C / Production host: Escherichia coli (E. coli) / Strain (production host): JM 109 / References: UniProt: Q45560
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
1411D-NOE
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 1H NMR SPECTROSCOPY. EXPERIMENTAL DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.

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Sample preparation

Sample conditionsIonic strength: 20 mM / pH: 6.5 / Pressure: 1 atm / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
Amber4.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
DYANAGuntert, Braun and Wuthrichstructure calculation
Amber4.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANstructure calculation
RefinementMethod: TORSION ANGLE DYNAMICS, RESTRAINED ENERGY MINIMIZATION, RESTRAINED MOLECULAR DYNAMICS
Software ordinal: 1
Details: THE STRUCTURE CALCULATIONS WERE CARRIED OUT WITH THE TORSION ANGLE DYNAMICS PROGRAM DYANA (BY GUENTERT,MUMENTHALER,WUETHRICH). THE 20 STRUCTURES OF THE DYANA FAMILY WITH THE LOWEST TARGET ...Details: THE STRUCTURE CALCULATIONS WERE CARRIED OUT WITH THE TORSION ANGLE DYNAMICS PROGRAM DYANA (BY GUENTERT,MUMENTHALER,WUETHRICH). 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. REFINEMENT DETAILSCAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 500 / Conformers submitted total number: 20

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