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- PDB-5fd1: CRYSTAL STRUCTURES OF OXIDIZED AND REDUCED AZOTOBACTER VINELANDII... -

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Basic information

Entry
Database: PDB / ID: 5fd1
TitleCRYSTAL STRUCTURES OF OXIDIZED AND REDUCED AZOTOBACTER VINELANDII FERREDOXIN AT PH 8 AND PH 6
ComponentsFERREDOXIN
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 / DNA binding / metal ion binding
Similarity search - Function
Ferredoxin, C-terminal / : / Domain of unknown function (DUF3470) / 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. ...Ferredoxin, C-terminal / : / Domain of unknown function (DUF3470) / 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-1
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsStout, C.D.
Citation
Journal: J.Biol.Chem. / Year: 1993
Title: Crystal structures of oxidized and reduced Azotobacter vinelandii ferredoxin at pH 8 and 6.
Authors: Stout, C.D.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Crystallographic Analysis of Two Site-Directed Mutants of Azotobacter Vinelandii Ferredoxin
Authors: Soman, J. / Iismaa, S. / Stout, C.D.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990
Title: Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement
Authors: Martin, A.E. / Burgess, B.K. / Stout, C.D. / Cash, V.L. / Dean, D.R. / Jensen, G.M. / Stephens, P.J.
#3: Journal: J.Mol.Biol. / Year: 1989
Title: Refinement of the 7 Fe Ferredoxin from Azotobacter at 1.9 Angstroms Resolution
Authors: Stout, C.D.
#4: Journal: J.Biol.Chem. / Year: 1988
Title: 7-Iron Ferredoxin Revisited
Authors: Stout, C.D.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: (4Fe-4S)-Cluster-Depleted Azotobacter Vinelandii Ferredoxin I. A New 3Fe Iron-Sulfur Protein
Authors: Stephens, P.J. / Morgan, T.V. / Devlin, F. / Penner-Hahn, J.E. / Hodgson, K.O. / Scott, R.A. / Stout, C.D. / Burgess, B.K.
#6: Journal: J.Biol.Chem. / Year: 1983
Title: Structure of Azotobacter Vinelandii 7Fe Ferredoxin. Amino Acid Sequence and Electron Density Maps of Residues
Authors: Howard, J.B. / Lorsbach, T.W. / Ghosh, D. / Melis, K. / Stout, C.D.
#7: Journal: J.Mol.Biol. / Year: 1982
Title: Iron-Sulfur Clusters and Protein Structure of Azotobacter Ferredoxin at 2.0 Angstroms Resolution
Authors: Ghosh, D. / O'Donnell, S. / Fureyjunior, W. / Robbins, A.H. / Stout, C.D.
#8: Journal: J.Biol.Chem. / Year: 1981
Title: Structure of a 7Fe Ferredoxin from Azotobacter Vinelandii
Authors: Ghosh, D. / Fureyjunior, W. / O'Donnell, S. / Stout, C.D.
#9: Journal: J.Biol.Chem. / Year: 1980
Title: Iron-Sulfur Clusters in Azotobacter Ferredoxin at 2.5 Angstroms Resolution
Authors: Stout, C.D. / Ghosh, D. / Pattabhi, V. / Robbins, A.H.
#10: Journal: Am.Cryst.Assoc.,Abstr.Papers (Winter Meeting) / Year: 1979
Title: Structure of the Iron-Sulfur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution
Authors: Stout, C.D.
#11: Journal: J.Biol.Chem. / Year: 1979
Title: Two Crystal Forms of Azotobacter Ferredoxin
Authors: Stout, C.D.
#12: Journal: Nature / Year: 1979
Title: Structure of the Iron-Sulphur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution
Authors: Stout, C.D.
History
DepositionJun 29, 1993Processing site: BNL
SupersessionOct 15, 1993ID: 4FD1
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7073
Polymers12,0601
Non-polymers6472
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.200, 55.200, 95.200
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


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-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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 Å3/Da / Density % sol: 59.06 %
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 2 ℃ / pH: 7.4 / Method: vapor diffusion / Details: Stout, C.D., (1979) J.Biol.Chem., 254, 3598.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-10 mg/mlprotein1drop
20.5 Mpotassium phosphate1drop
31.2 Mammonium sulfate1drop
43.5 Mammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. all: 12058 / Num. obs: 9775 / % possible obs: 81.1 % / Num. measured all: 140232 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2.1 Å / % possible obs: 47.9 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.215 -
obs0.215 9586
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms841 0 15 30 886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.31
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.2 Å2
Refine LS restraints
*PLUS
Type: x_plane_restr / Dev ideal: 1.58

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