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- PDB-1fd2: SITE-DIRECTED MUTAGENESIS OF AZOTOBACTER VINELANDII FERREDOXIN I.... -

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Basic information

Entry
Database: PDB / ID: 1fd2
TitleSITE-DIRECTED MUTAGENESIS OF AZOTOBACTER VINELANDII FERREDOXIN I. (FE-S) CLUSTER-DRIVEN PROTEIN REARRANGEMENT
ComponentsFERREDOXIN
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. ...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: 1.9 Å
AuthorsStout, C.D.
Citation
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.
#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: J.Mol.Biol. / Year: 1989
Title: Refinement of the 7 Fe Ferredoxin from Azotobacter at 1.9 Angstroms Resolution
Authors: Stout, C.D.
#3: Journal: J.Biol.Chem. / Year: 1988
Title: 7-Iron Ferredoxin Revisited
Authors: Stout, C.D.
#4: 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.
#5: 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.
#6: 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.
#7: 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.
#8: 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.
#9: 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.
#10: Journal: J.Biol.Chem. / Year: 1979
Title: Two Crystal Forms of Azotobacter Ferredoxin
Authors: Stout, C.D.
#11: Journal: Nature / Year: 1979
Title: Structure of the Iron-Sulphur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution
Authors: Stout, C.D.
History
DepositionDec 8, 1988Processing site: BNL
Revision 1.0Oct 15, 1989Provider: 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_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_database_status.process_site / _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)12,6753
Polymers12,0271
Non-polymers6472
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.000, 55.000, 95.400
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: 12027.466 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.: 31 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE OF THIS MUTANT IS THE SAME AS THAT OF THE NATIVE EXEPT THAT RESIDUE 20 HAS CHANGED ...THE STRUCTURE OF THIS MUTANT IS THE SAME AS THAT OF THE NATIVE EXEPT THAT RESIDUE 20 HAS CHANGED FROM CYS TO ALA. THIS PROTEIN HAS A CUBANE-LIKE (3FE-4S) CLUSTER AND ALSO A STANDARD (4FE-4S) CLUSTER. THE (4FE-4S) CLUSTER HAS CYS 24 AS A LIGAND INSTEAD OF CYS 20 (NOW ALA 20) AND THE STRUCTURE IS REARRANGED AROUND THIS CLUSTER, ESPECIALLY AT RESIDUES 22 - 24. THE OTHER LIGANDS OF THE (4FE-4S) REMAIN THE SAME.

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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: 58.96 %
Crystal grow
*PLUS
Temperature: 2 ℃ / pH: 7.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-10 mg/mlprotein11
20.5 Mpotassium phosphate11
31.2 Mammonium sulfate11
43.5 Mammonium sulfate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. all: 11697 / Num. measured all: 55860 / Rmerge F obs: 0.095

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.9→8 Å /
RfactorNum. reflection
Rwork0.232 -
obs-9792
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 15 31 886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_angle_deg3.67
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.67

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