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- PDB-2zvs: Crystal structure of the 2[4FE-4S] ferredoxin from escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2zvs
TitleCrystal structure of the 2[4FE-4S] ferredoxin from escherichia coli
ComponentsUncharacterized ferredoxin-like protein yfhL
KeywordsELECTRON TRANSPORT / FERREDOXIN / [4FE-4S] CLUSTERS / IRON-SULFUR CLUSTERS / ESCHERICHIA COLI / reduction potential / Iron binding protein / Iron / Metal-binding
Function / homology
Function and homology information


tRNA wobble base modification / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
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 YfhL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGiastas, P. / Mavridis, M.I.
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
DepositionNov 18, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / 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_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: Uncharacterized ferredoxin-like protein yfhL
B: Uncharacterized ferredoxin-like protein yfhL
C: Uncharacterized ferredoxin-like protein yfhL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1269
Polymers29,0163
Non-polymers2,1106
Water3,225179
1
A: Uncharacterized ferredoxin-like protein yfhL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3753
Polymers9,6721
Non-polymers7032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized ferredoxin-like protein yfhL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3753
Polymers9,6721
Non-polymers7032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized ferredoxin-like protein yfhL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3753
Polymers9,6721
Non-polymers7032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.543, 65.543, 132.367
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11B-92-

HOH

21B-104-

HOH

Detailsthe biological unit is unknown.

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Components

#1: Protein Uncharacterized ferredoxin-like protein yfhL


Mass: 9672.118 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: yfhL / Plasmid: pGP1-2 / Production host: Escherichia coli (E. coli) / Strain (production host): K38 / References: UniProt: P52102
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.83 Å3/Da / Density % sol: 56.52 % / Description: The file contains Friedel pair.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.5M CACL2, 0.1M TRIS-HCL, 20% PEG 4000, pH 9.0, 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 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 71543 / Observed criterion σ(F): 4 / Redundancy: 5.8 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.066
Reflection shellResolution: 1.65→1.68 Å / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

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

1blu


Resolution: 1.65→30 Å / Num. parameters: 8484 / Num. restraintsaints: 8348 / Isotropic thermal model: ISOTROPIC / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: Engh & Huber
Details: The file contains Friedel pair. Used weighted CONJUGATED GRADIENT MATRIX least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.2732 2080 2.9 %THIN SHELLS
Rwork0.2034 ---
all0.2114 71543 --
obs0.2106 71543 100 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2042
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 48 179 2121
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0.061
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0345
X-RAY DIFFRACTIONs_zero_chiral_vol0.105
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.113
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.128
X-RAY DIFFRACTIONs_approx_iso_adps0

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