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Yorodumi- PDB-3i8x: Structure of the cytosolic domain of E. coli FeoB, GDP-bound form -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i8x | ||||||
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Title | Structure of the cytosolic domain of E. coli FeoB, GDP-bound form | ||||||
Components | Ferrous iron transport protein B | ||||||
Keywords | TRANSPORT PROTEIN / GTPase / GPCR / iron uptake / Feo / Cell inner membrane / Cell membrane / GTP-binding / Ion transport / Iron / Iron transport / Membrane / Nucleotide-binding / Transmembrane / Transport | ||||||
Function / homology | Function and homology information iron ion import across plasma membrane / ferrous iron transmembrane transporter activity / DNA damage response / GTP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Petermann, N. / Hansen, G. / Hogg, T. / Hilgenfeld, R. | ||||||
Citation | Journal: To be Published Title: Structural basis for the intrinsic GTPase and GDI activities of FeoB, a prokaryotic transmembrane GTP/GDP-binding protein Authors: Petermann, N. / Schmidt, C.L. / Hansen, G. / Wagner, A.K. / Hilgenfeld, R. / Hogg, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i8x.cif.gz | 167.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i8x.ent.gz | 133.2 KB | Display | PDB format |
PDBx/mmJSON format | 3i8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/3i8x ftp://data.pdbj.org/pub/pdb/validation_reports/i8/3i8x | HTTPS FTP |
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-Related structure data
Related structure data | 3i8sSC 3i92C 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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Unit cell |
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-Components
#1: Protein | Mass: 30086.350 Da / Num. of mol.: 3 / Fragment: Cytosolic domain (UNP residues 1-274) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b3409, feoB, JW3372 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(placI) / References: UniProt: P33650 #2: Chemical | #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: 2.11 Å3/Da / Density % sol: 41.6 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion / pH: 4.9 Details: 10 % PEG 4000, 100 mM Na-malonate, pH 4.9, VAPOR DIFFUSION, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9085 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2007 |
Radiation | Monochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9085 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→25.15 Å / Num. obs: 35991 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3I8S Resolution: 2.25→25.14 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.573 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.955 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→25.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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