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- PDB-4fxc: TERTIARY STRUCTURE OF [2FE-2S] FERREDOXIN FROM SPIRULINA PLATENSI... -

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Basic information

Entry
Database: PDB / ID: 4fxc
TitleTERTIARY STRUCTURE OF [2FE-2S] FERREDOXIN FROM SPIRULINA PLATENSIS REFINED AT 2.5 ANGSTROMS RESOLUTION: STRUCTURAL COMPARISONS OF PLANT-TYPE FERREDOXINS AND AN ELECTROSTATIC POTENTIAL ANALYSIS
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) ...Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesArthrospira platensis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsFukuyama, K. / Tsukihara, T.
Citation
Journal: J.Biochem.(Tokyo) / Year: 1995
Title: Tertiary structure of [2Fe-2S] ferredoxin from Spirulina platensis refined at 2.5 A resolution: structural comparisons of plant-type ferredoxins and an electrostatic potential analysis.
Authors: Fukuyama, K. / Ueki, N. / Nakamura, H. / Tsukihara, T. / Matsubara, H.
#1: Journal: J.Biochem.(Tokyo) / Year: 1981
Title: X-Ray Analysis of a (2Fe-2S) Ferredoxin from Spirulina Platensis. Main Chain Fold and Location of Side Chains at 2.5 Angstroms Resolution
Authors: Tsukihara, T. / Fukuyama, K. / Nakamura, M. / Katsube, Y. / Tanaka, N. / Kakudo, M. / Wada, K. / Hase, T. / Matsubara, H.
#2: Journal: Nature / Year: 1980
Title: Structure of S. Platensis (2Fe-2S) Ferredoxin and Evolution of Chloroplast-Type Ferredoxins
Authors: Fukuyama, K. / Hase, T. / Matsumoto, S. / Tsukihara, T. / Katsube, Y. / Tanaka, N. / Kakudo, M. / Wada, K. / Matsubara, H.
#3: Journal: J.Biochem.(Tokyo) / Year: 1978
Title: X-Ray Analysis of Ferredoxin from Spirulina Platensis. II. Chelate Structure of Active Center
Authors: Tsukihara, T. / Fukuyama, K. / Tahara, H. / Katsube, Y. / Matsuura, Y. / Tanaka, N. / Kakudo, M. / Wada, K. / Matsubara, H.
#5: Journal: J.Biochem.(Tokyo) / Year: 1977
Title: Location of the Iron-Sulfur Cluster in Spirulina Platensis Ferredoxin by X-Ray Analysis
Authors: Ogawa, K. / Tsukihara, T. / Tahara, H. / Katsube, Y. / Matsu-Ura, Y. / Tanaka, N. / Kakudo, M. / Wada, K. / Matsubara, H.
#4: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1978
History
DepositionApr 25, 1995Processing site: BNL
SupersessionDec 7, 1995ID: 3FXC
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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)10,6822
Polymers10,5061
Non-polymers1761
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.320, 28.510, 108.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein FERREDOXIN


Mass: 10506.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis (bacteria) / References: UniProt: P00246
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal grow
*PLUS
Temperature: 3 ℃ / pH: 7.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11-3 %protein11
287 %satammonium sulfate12
30.5 M12NaCl
40.1 MTris-HCl12

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.199 --
obs0.199 2912 84.6 %
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms732 0 4 42 778
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.022
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_deg
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_it2.62.6
X-RAY DIFFRACTIONx_mcangle_it3.93.9
X-RAY DIFFRACTIONx_scbond_it3.43.4
X-RAY DIFFRACTIONx_scangle_it4.84.8
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d0.072
X-RAY DIFFRACTIONx_plane_restr0.031
X-RAY DIFFRACTIONx_chiral_restr0.162
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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