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- PDB-2fd2: CRYSTALLOGRAPHIC ANALYSIS OF TWO SITE-DIRECTED MUTANTS OF AZOTOBA... -

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Basic information

Entry
Database: PDB / ID: 2fd2
TitleCRYSTALLOGRAPHIC ANALYSIS OF TWO SITE-DIRECTED MUTANTS OF AZOTOBACTER VINELANDII FERREDOXIN
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. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits ...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: 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.
#1: 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.
#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
DepositionAug 20, 1990Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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
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: 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 / Iron–sulfur cluster


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


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#4: Water ChemComp-HOH / water / 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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal grow
*PLUS
pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11 mM1reservoirNa2S2O4
20.1 MTris-HCl1drop
34.8 M1drop(NH4)2SO4
41 mM1dropNa2S2O4for crystals mounted anaerobically

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Data collection

Reflection
*PLUS
Highest resolution: 1.99 Å / Lowest resolution: 9999 Å / Num. all: 10564 / Num. obs: 9084 / % possible obs: 86 % / Observed criterion σ(I): 15.5 / Num. measured all: 108979 / Rmerge(I) obs: 0.121

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.9→8 Å /
RfactorNum. reflection
Rwork0.232 -
obs-8379
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 15 30 885
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.65
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
Highest resolution: 1.99 Å / Lowest resolution: 8 Å / Num. reflection all: 8379 / σ(F): 0 / Rfactor all: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.65

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