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- PDB-3exy: Crystal structure of the 2[4Fe-4S] ferredoxin V13G variant from a... -

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Basic information

Entry
Database: PDB / ID: 3exy
TitleCrystal structure of the 2[4Fe-4S] ferredoxin V13G variant from allochromatium vinosum
ComponentsFerredoxin
KeywordsELECTRON TRANSPORT / FERREDOXIN / [4FE-4S] CLUSTERS / 4Fe-4S / Iron / Iron-sulfur / Metal-binding / Transport
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
: / 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 / Ferredoxin
Similarity search - Component
Biological speciesAllochromatium vinosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsGiastas, P. / Saridakis, E. / Mavridis, I.M.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2009
Title: Insight into the protein and solvent contributions to the reduction potentials of [4Fe-4S]2+/+ clusters: crystal structures of the Allochromatium vinosum ferredoxin variants C57A and V13G and ...Title: Insight into the protein and solvent contributions to the reduction potentials of [4Fe-4S]2+/+ clusters: crystal structures of the Allochromatium vinosum ferredoxin variants C57A and V13G and the homologous Escherichia coli ferredoxin.
Authors: Saridakis, E. / Giastas, P. / Efthymiou, G. / Thoma, V. / Moulis, J.M. / Kyritsis, P. / Mavridis, I.M.
History
DepositionOct 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7253
Polymers9,0221
Non-polymers7032
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.425, 51.425, 76.425
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-151-

HOH

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Components

#1: Protein Ferredoxin


Mass: 9021.926 Da / Num. of mol.: 1 / Mutation: V13G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium vinosum (bacteria) / Gene: fdx / Production host: Escherichia coli (E. coli) / References: UniProt: P00208
#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.: 169 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.96 %
Crystal growTemperature: 277 K / pH: 8
Details: 3.5M AMMONIUM SULPHATE, 0.3 M SODIUM CHLORIDE, 0.1 M TRIS , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81
DetectorType: MARREASEARCH / Detector: CCD / Date: Jun 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. obs: 18180 / % possible obs: 95.2 % / Redundancy: 3.3 %
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 3.3 % / % possible all: 97.2

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BLU

1blu


Resolution: 1.48→30 Å / Num. parameters: 6375 / Num. restraintsaints: 7161 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.2177 1017 5.6 %THIN SHELLS
Rwork0.162 ---
all0.1702 18070 --
obs0.162 18070 90.2 %-
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 753.75
Refinement stepCycle: LAST / Resolution: 1.48→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms627 0 16 169 812
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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