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- PDB-1fer: STRUCTURE AT PH 6.5 OF FERREDOXIN I FROM AZOTOBACTER VINELANDII A... -

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Basic information

Entry
Database: PDB / ID: 1fer
TitleSTRUCTURE AT PH 6.5 OF FERREDOXIN I FROM AZOTOBACTER VINELANDII AT 2.3 ANGSTROMS RESOLUTION
ComponentsFERREDOXIN I
KeywordsELECTRON TRANSFER(IRON-SULFUR PROTEIN)
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / DNA binding / metal ion binding
Similarity search - Function
Ferredoxin, C-terminal / Domain of unknown function (DUF3470) / 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 ...Ferredoxin, C-terminal / Domain of unknown function (DUF3470) / 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
FE3-S4 CLUSTER / IRON/SULFUR CLUSTER / Ferredoxin-1
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsMerritt, E.A. / Stout, G.H. / Turley, S. / Sieker, L.C. / Jensen, L.H. / Orme-Johnson, W.H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure at pH 6.5 of ferredoxin I from Azotobacter vinelandii at 2.3 A resolution.
Authors: Merritt, E.A. / Stout, G.H. / Turley, S. / Sieker, L.C. / Jehsen, L.H. / Orme-Johnson, W.H.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Structure of Ferredoxin I from Azotobacter Vinelandii
Authors: Stout, G.H. / Turley, S. / Sieker, L.C. / Jensen, L.H.
History
DepositionSep 2, 1992Processing site: BNL
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX HELIX ASSIGNMENTS WERE BASED ON ANALYSIS USING PROGRAM *DSSP* OF W. KABSCH AND C. SANDER.

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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)12,7073
Polymers12,0601
Non-polymers6472
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.550, 55.550, 95.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein FERREDOXIN I


Mass: 12059.530 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / References: UniProt: P00214
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal grow
*PLUS
Temperature: 277 K / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 %protein1drop
20.15 MTris-maleate1reservoir
370 %sat1reservoir(NH4)2SO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Num. obs: 7099 / Rmerge(I) obs: 3

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.17 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms853 0 15 98 966
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
X-RAY DIFFRACTIONx_angle_deg3.1
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 10 Å / Num. reflection obs: 6986 / Rfactor obs: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.1
X-RAY DIFFRACTIONx_angle_deg3.1

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