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- PDB-1fxr: CRYSTAL STRUCTURE OF THE FERREDOXIN I FROM DESULFOVIBRIO AFRICANU... -

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Basic information

Entry
Database: PDB / ID: 1fxr
TitleCRYSTAL STRUCTURE OF THE FERREDOXIN I FROM DESULFOVIBRIO AFRICANUS AT 2.3 ANGSTROMS RESOLUTION
ComponentsFERREDOXIN I
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding
Similarity search - Function
: / 3Fe-4S ferredoxin / 4Fe-4S single cluster domain of Ferredoxin I / Alpha-Beta Plaits - #20 / 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 / Ferredoxin-1
Similarity search - Component
Biological speciesDesulfovibrio africanus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsFrey, M. / Roth, M.
CitationJournal: Biochemistry / Year: 1994
Title: Crystal structure of the ferredoxin I from Desulfovibrio africanus at 2.3 A resolution.
Authors: Sery, A. / Housset, D. / Serre, L. / Bonicel, J. / Hatchikian, C. / Frey, M. / Roth, M.
History
DepositionNov 14, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: 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

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Assembly

Deposited unit
A: FERREDOXIN I
B: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2135
Polymers14,4142
Non-polymers7993
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-60 kcal/mol
Surface area7000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.600, 58.100, 20.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999092, 0.042575, 0.00141), (0.042595, 0.998872, 0.020999), (-0.000514, 0.02104, -0.999779)
Vector: -21.23436, 0.23631, 20.56958)

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Components

#1: Protein FERREDOXIN I


Mass: 7206.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio africanus (bacteria) / References: UniProt: P00210
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.01 Å3/Da / Density % sol: 38.93 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
126.6 mg/mlprotein1drop
253-65 %satammonium sulfate1reservoir
30.1 Msodium acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / % possible obs: 70.6 % / Rmerge(I) obs: 0.086

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→10 Å / σ(F): 2
RfactorNum. reflection
Rfree0.227 -
Rwork0.182 -
obs0.182 4815
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 21 70 1091
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.93
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: 0.182 / Rfactor Rfree: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.93
X-RAY DIFFRACTIONx_dihedral_angle_d24.79
X-RAY DIFFRACTIONx_dihedral_angle_deg1.22

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