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- PDB-1fdn: REFINED CRYSTAL STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CLOSTR... -

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Basic information

Entry
Database: PDB / ID: 1fdn
TitleREFINED CRYSTAL STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CLOSTRIDIUM ACIDURICI AT 1.84 ANGSTROMS RESOLUTION
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / cytoplasm
Similarity search - Function
7Fe ferredoxin / Alpha-Beta Plaits - #20 / : / 4Fe-4S dicluster 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
IRON/SULFUR CLUSTER / 4Fe-4S ferredoxin FdxA
Similarity search - Component
Biological speciesClostridium acidurici (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.84 Å
AuthorsDuee, E. / Fanchon, E. / Vicat, J. / Sieker, L.C. / Meyer, J. / Moulis, J-M.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Refined crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici at 1.84 A resolution.
Authors: Duee, E.D. / Fanchon, E. / Vicat, J. / Sieker, L.C. / Meyer, J. / Moulis, J.M.
#1: Journal: Biochem.J. / Year: 1993
Title: Sequences of Clostridial Ferredoxins
Authors: Meyer, J. / Moulis, J.-M. / Scherrer, N. / Gagnon, J. / Ulrich, J.
#2: Journal: J.Biol.Chem. / Year: 1988
Title: Crystal Structure of Clostridium Acidi-Urici Ferredoxin at 5 Angstroms Resolution Based on Measurements of Anomalous X-Ray Scattering at Multiple Wavelengths
Authors: Krishnamurthy, H.M. / Hendrickson, W.A. / Orme-Johnson, W.H. / Merritt, E.A. / Phizackerley, R.P.
History
DepositionMar 31, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: 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_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)6,2433
Polymers5,5401
Non-polymers7032
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.440, 34.440, 74.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: TWO ALTERNATE POSITIONS FOR THE SIDE CHAIN OF ASN 21 HAVE BEEN OBSERVED AND GIVEN OCCUPANCIES OF 0.5.
2: THE EXACT POSITIONS OF ASP 27 AND ASP 28 ARE UNDEFINED FROM THE X-RAY DATA. THESE RESIDUES HAVE BEEN BUILT WITH A GOOD GEOMETRY FOR THE MAIN CHAIN AND REASONABLE CHI ANGLES FOR THE SIDE CHAINS.

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Components

#1: Protein FERREDOXIN


Mass: 5540.179 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acidurici (bacteria) / References: UniProt: P00198
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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 Å3/Da / Density % sol: 38.49 %
Crystal grow
*PLUS
Temperature: 281 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
155-60 %satammonium sulfate1reservoir
2100 mMTrisMaleate1reservoir
310 mg/mlprotein1drop
455-60 %satammonium sulfate1drop
5100 mMTrisMaleate1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 4203 / % possible obs: 92 % / Num. measured all: 15645 / Rmerge F obs: 0.062

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.84→18 Å / σ(F): 2
Details: THE EXACT POSITIONS OF ASP 27 AND ASP 28 ARE UNDEFINED FROM THE X-RAY DATA. THESE RESIDUES HAVE BEEN BUILT WITH A GOOD GEOMETRY FOR THE MAIN CHAIN AND REASONABLE CHI ANGLES FOR THE SIDE CHAINS.
RfactorNum. reflection
Rwork0.169 -
obs0.169 3772
Refinement stepCycle: LAST / Resolution: 1.84→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms383 0 16 46 445
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.58
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.58

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