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Yorodumi- PDB-2zvs: Crystal structure of the 2[4FE-4S] ferredoxin from escherichia coli -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zvs | ||||||
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Title | Crystal structure of the 2[4FE-4S] ferredoxin from escherichia coli | ||||||
Components | Uncharacterized ferredoxin-like protein yfhL | ||||||
Keywords | ELECTRON TRANSPORT / FERREDOXIN / [4FE-4S] CLUSTERS / IRON-SULFUR CLUSTERS / ESCHERICHIA COLI / reduction potential / Iron binding protein / Iron / Metal-binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Giastas, P. / Mavridis, M.I. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zvs.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zvs.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zvs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/2zvs ftp://data.pdbj.org/pub/pdb/validation_reports/zv/2zvs | HTTPS FTP |
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-Related structure data
Related structure data | 3eunC 3exyC 1bluS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | the biological unit is unknown. |
-Components
#1: Protein | 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 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.52 % / Description: The file contains Friedel pair. |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.65→1.68 Å / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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.
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2042 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→30 Å
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Refine LS restraints |
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