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- PDB-1dax: OXIDISED DESULFOVIBRIO AFRICANUS FERREDOXIN I, NMR, MINIMIZED AVE... -

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Basic information

Entry
Database: PDB / ID: 1dax
TitleOXIDISED DESULFOVIBRIO AFRICANUS FERREDOXIN I, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsFERREDOXIN I
KeywordsELECTRON TRANSPORT / OXIDISED DESULFOVIBRIO AFRICANUS FERREDOXIN I / ELECTRON-TRANSFER PROTEIN / 4FE-4S CLUSTER
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding
Similarity search - Function
4Fe-4S single cluster domain of Ferredoxin I / 3Fe-4S ferredoxin / Alpha-Beta Plaits - #20 / 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-1
Similarity search - Component
Biological speciesDesulfovibrio africanus (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, DG-SIMULATED ANNEALING
AuthorsDavy, S.L. / Osborne, M.J. / Moore, G.R.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Determination of the structure of oxidised Desulfovibrio africanus ferredoxin I by 1H NMR spectroscopy and comparison of its solution structure with its crystal structure.
Authors: Davy, S.L. / Osborne, M.J. / Moore, G.R.
History
DepositionDec 1, 1997Processing site: BNL
Revision 1.0Jan 13, 1999Provider: 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: Database references / Derived calculations ...Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_exptl_sample_conditions / pdbx_struct_assembly / 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_exptl_sample_conditions.pressure_units / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5592
Polymers7,2071
Non-polymers3521
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 75
Representative

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Components

#1: Protein FERREDOXIN I /


Mass: 7206.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: OXIDIZED / Source: (natural) Desulfovibrio africanus (bacteria) / Strain: BENGHAZI / References: UniProt: P00210
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / 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
111DQF-COSY
121TOCSY
131NOESY
1411D NOE
NMR detailsText: THE STRUCTURES WERE OBTAINED USING 1H-1H 2D NMR EXPERIMENTS (DQF-COSY, TOCSY, NOESY). ADDITIONALLY 1D NOE EXPERIMENTS PROVIDED INFORMATION ON THE REGIONS OF THE PROTEIN CLOSE TO THE PARAMAGNETIC 4FE-4S CLUSTER.

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Sample preparation

DetailsContents: 90%H2O/10%D2O, 99.9%D2O
Sample conditionspH: 7.2 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
JEOL JEOL GX 400JEOLJEOL GX 4004001
Bruker JEOL A 500BrukerJEOL A 5005002
Varian BRUKER AMX500 AND AMX600VarianBRUKER AMX500 AND AMX6006003
Varian VARIAN UNITY INOVA 600VarianVARIAN UNITY INOVA 6006004

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameVersionDeveloperClassification
DIANA2.5GUNTERT,WUTHRICHrefinement
DIANA2.5structure solution
X-PLOR3.843structure solution
RefinementMethod: DISTANCE GEOMETRY, DG-SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformers calculated total number: 75 / Conformers submitted total number: 1

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