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Yorodumi- PDB-2eff: Crystal structure analysis of the complex between CyaY and Co(II) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eff | ||||||
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Title | Crystal structure analysis of the complex between CyaY and Co(II) | ||||||
Components | Protein cyaY | ||||||
Keywords | UNKNOWN FUNCTION / FRATAXIN / FRIEDREICH'S ATAXIA IRON BINDING / IRON-SULFUR CLUSTER ASSEMBLY / DETOXIFYING REDOX-ACTIVE IRON | ||||||
Function / homology | Function and homology information iron chaperone activity / iron-sulfur cluster assembly / ferroxidase activity / ferric iron binding / ferrous iron binding / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sica, F. / Franzese, M. | ||||||
Citation | Journal: Febs J. / Year: 2007 Title: Understanding the binding properties of an unusual metal-binding protein - a study of bacterial frataxin Authors: Pastore, C. / Franzese, M. / Sica, F. / Temussi, P. / Pastore, A. #1: Journal: Structure / Year: 2004 Title: Solution structure of the bacterial frataxin ortholog, CyaY: mapping the iron binding sites Authors: Nair, M. / Adinolfi, S. / Pastore, C. / Kelly, G. / Temussi, P. / Pastore, A. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Crystal structure of Escherichia coli CyaY protein reveals a previously unidentified fold for the evolutionarily conserved frataxin family Authors: Cho, S.J. / Lee, M.G. / Yang, J.K. / Lee, J.Y. / Song, H.K. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eff.cif.gz | 37.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eff.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 2eff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2eff_validation.pdf.gz | 431.8 KB | Display | wwPDB validaton report |
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Full document | 2eff_full_validation.pdf.gz | 433.1 KB | Display | |
Data in XML | 2eff_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 2eff_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/2eff ftp://data.pdbj.org/pub/pdb/validation_reports/ef/2eff | HTTPS FTP |
-Related structure data
Related structure data | 2p1xC 1ew4S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12242.358 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CYAY, B3807 / Plasmid: pET22b-CyaY / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27838 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7 Details: 30% w/v PEG 4000, 200mM CoCl2, 2mM beta-mercaptoethanol, 100 mM sodium acetate, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Nov 8, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 20336 / % possible obs: 99.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 5 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 6.9 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1EW4 Resolution: 1.8→18.6 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→18.6 Å
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Refine LS restraints |
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