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Yorodumi- PDB-7r7b: 1.50 Angstroem Crystal Structure of FeoA from Bacteroides fragilis -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r7b | ||||||
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Title | 1.50 Angstroem Crystal Structure of FeoA from Bacteroides fragilis | ||||||
Components | Ferrous iron transport protein B | ||||||
Keywords | METAL TRANSPORT / Feo / SH3 / membrane transporter | ||||||
Function / homology | Function and homology information : / ferrous iron transmembrane transporter activity / transition metal ion binding / membrane => GO:0016020 / GTP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bacteroides fragilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Sestok, A.E. / Smith, A.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: A fusion of the Bacteroides fragilis ferrous iron import proteins reveals a role for FeoA in stabilizing GTP-bound FeoB. Authors: Sestok, A.E. / Brown, J.B. / Obi, J.O. / O'Sullivan, S.M. / Garcin, E.D. / Deredge, D.J. / Smith, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r7b.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r7b.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 7r7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/7r7b ftp://data.pdbj.org/pub/pdb/validation_reports/r7/7r7b | HTTPS FTP |
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-Related structure data
Related structure data | 2k5lS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 8674.333 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) Gene: feoB, BUN20_04310, DW228_07360, DXB57_02360, EC80_0207810, EE52_0204010, EE52_020515, FOC69_09580, IA74_010110, IB64_011160 Production host: Escherichia coli (E. coli) / References: UniProt: A0A081U6Q6 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.07 Å3/Da / Density % sol: 40.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M di-potassium phosphate, 2.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→46.16 Å / Num. obs: 23079 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 14.65 Å2 / CC1/2: 0.992 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 1138 / CC1/2: 0.529 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2K5L Resolution: 1.5→36.03 Å / SU ML: 0.2059 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8118 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→36.03 Å
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Refine LS restraints |
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LS refinement shell |
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