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- PDB-1fdd: AZOTOBACTER VINELANDII FERREDOXIN I: ASPARTATE 15 FACILITATES PRO... -

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Basic information

Entry
Database: PDB / ID: 1fdd
TitleAZOTOBACTER VINELANDII FERREDOXIN I: ASPARTATE 15 FACILITATES PROTON TRANSFER TO THE REDUCED [3FE-4S] CLUSTER
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: Azotobacter vinelandii ferredoxin I. Aspartate 15 facilitates proton transfer to the reduced [3Fe-4S] cluster.
Authors: Shen, B. / Martin, L.L. / Butt, J.N. / Armstrong, F.A. / Stout, C.D. / Jensen, G.M. / Stephens, P.J. / La Mar, G.N. / Gorst, C.M. / Burgess, B.K.
#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
DepositionJan 17, 1993Processing site: BNL
Revision 1.0Oct 31, 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_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

Downloads & links

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Assembly

Deposited unit
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7063
Polymers12,0591
Non-polymers6472
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.600, 55.600, 95.900
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: 12058.546 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.: 23 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CHEMICAL SEQUENCE WAS DETERMINED IN COLLABORATION WITH J. B. HOWARD AND T. LORSBACH OF DEPT. OF ...THE CHEMICAL SEQUENCE WAS DETERMINED IN COLLABORATION WITH J. B. HOWARD AND T. LORSBACH OF DEPT. OF BIOCHEMISTRY, UNIVERSITY OF MINNESOTA, ST. PAUL, MINNESOTA. SUBSEQUENT WORK ON THIS STRUCTURE YIELDED SEQUENCE CHANGES 1. GLY 62 CHANGED TO GLU 62 2. ASP 76 CHANGED TO GLU 76 3. VAL 107 DELETED (REPLACED BY WATER MOLECULES)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 2 ℃ / pH: 7.4 / Method: vapor diffusion / Details: referred to J.Biol.Chem. 254.3598-3599 1979
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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. all: 12536 / Num. obs: 11181 / % possible obs: 89 % / Num. measured all: 59292 / Rmerge(I) obs: 0.0595

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.207 -
obs0.207 10792
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms841 0 15 23 879
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg3.42
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: 1.9 Å / Lowest resolution: 8 Å / Num. reflection all: 10792 / σ(F): 0 / Rfactor all: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.42

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