+Open data
-Basic information
Entry | Database: PDB / ID: 3o72 | ||||||
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Title | Crystal structure of EfeB in complex with heme | ||||||
Components | Redox component of a tripartite ferrous iron transporter | ||||||
Keywords | HEME-BINDING PROTEIN / EfeB in complex with heme / Heme deferrochelatase / Heme binding | ||||||
Function / homology | Function and homology information iron import into cell / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / periplasmic space / hydrolase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Liu, X. / Du, Q. / Wang, Z. / Zhu, D. / Huang, Y. / Li, N. / Xu, S. / Gu, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystal structure and biochemical features of EfeB/YcdB from Escherichia coli O157: ASP235 plays divergent roles in different enzyme-catalyzed processes Authors: Liu, X. / Du, Q. / Wang, Z. / Zhu, D. / Huang, Y. / Li, N. / Wei, T. / Xu, S. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o72.cif.gz | 326.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o72.ent.gz | 274.6 KB | Display | PDB format |
PDBx/mmJSON format | 3o72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o72_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3o72_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3o72_validation.xml.gz | 67.3 KB | Display | |
Data in CIF | 3o72_validation.cif.gz | 95.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/3o72 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/3o72 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 44411.957 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 strain TW1435 / Gene: efeB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6UPP3, UniProt: Q8XAS4*PLUS #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-OXY / #4: 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: 2.15 Å3/Da / Density % sol: 42.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: 20% PEG 3350, 0.2M ammonium chloride, pH 8.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å | |||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2009 | |||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.95→50 Å / Num. all: 104514 / Num. obs: 104514 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 20.4 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→50 Å / SU ML: 0.23 / σ(F): 0.05 / σ(I): 0.05 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.271 Å2 / ksol: 0.329 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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