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

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Basic information

Entry
Database: PDB / ID: 1bqx
TitleARTIFICIAL FE8S8 FERREDOXIN: THE D13C VARIANT OF BACILLUS SCHLEGELII FE7S8 FERREDOXIN
ComponentsPROTEIN (FERREDOXIN)
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
DepositionAug 20, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 26, 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 / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _pdbx_nmr_software.name / _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
Revision 2.2May 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: PROTEIN (FERREDOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4423
Polymers8,7391
Non-polymers7032
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 500LEAST RESTRAINT VIOLATIONS
Representative

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Components

#1: Protein 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


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: MINIMIZED AVERAGE STRUCTURE. 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 AVANCE500BrukerAVANCE5005001
Bruker AVANCE600BrukerAVANCE6006002
Bruker AVANCE800BrukerAVANCE8008003

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Processing

NMR software
NameVersionDeveloperClassification
Amber4.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
DYANAstructure solution
Amberstructure solution
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. 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 ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS / Conformers calculated total number: 500 / Conformers submitted total number: 1

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