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- PDB-1fca: STRUCTURE OF THE FERREDOXIN FROM CLOSTRIDIUM ACIDURICI: MODEL AT ... -

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Basic information

Entry
Database: PDB / ID: 1fca
TitleSTRUCTURE OF THE FERREDOXIN FROM CLOSTRIDIUM ACIDURICI: MODEL AT 1.8 ANGSTROMS RESOLUTION
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT (CYTOCHROME)
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
7Fe ferredoxin / 4Fe-4S binding domain / 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: 1.8 Å
AuthorsTranqui, D. / Jesior, J.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of the ferredoxin from Clostridium acidurici: model at 1.8 A resolution.
Authors: TranQui, D. / Jesior, J.C.
History
DepositionSep 23, 1994Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)6,1993
Polymers5,4961
Non-polymers7032
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.441, 34.441, 74.778
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-100-

HOH

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Components

#1: Protein FERREDOXIN /


Mass: 5496.168 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 / Iron–sulfur cluster


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


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Details: Murthy, H. M. K., (1988) J. Biol. Chem., 263, 18430.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
2100 mMTris-HCl1drop
346-52 %satammonium sulfate1drop
465-74 %satammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→5 Å / Num. obs: 4500 / % possible obs: 80.3 %
Reflection shell
*PLUS
Num. unique obs: 3921 / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→5 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.143 -
obs0.143 15645
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms447 0 16 45 508

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