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Yorodumi- PDB-9d8d: Crystal structure of Vibrio cholerae NFeoB in the GMPPCP-bound form -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9d8d | |||||||||
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| Title | Crystal structure of Vibrio cholerae NFeoB in the GMPPCP-bound form | |||||||||
Components | Ferrous iron transport protein B | |||||||||
Keywords | TRANSPORT PROTEIN / Feo / iron / transport | |||||||||
| Function / homology | Function and homology informationferrous iron transmembrane transporter activity / GTP binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | |||||||||
Authors | Lee, M. / Magante, K.D. / Smith, A.T. | |||||||||
| Funding support | United States, 2items
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Citation | Journal: To Be PublishedTitle: Crystal structure of Vibrio cholerae NFeoB in the GMPPCP-bound form Authors: Lee, M. / Magante, K.D. / Smith, A.T. | |||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9d8d.cif.gz | 409.3 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9d8d.ent.gz | 337.6 KB | Display | PDB format |
| PDBx/mmJSON format | 9d8d.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9d8d_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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| Full document | 9d8d_full_validation.pdf.gz | 1.5 MB | Display | |
| Data in XML | 9d8d_validation.xml.gz | 46.6 KB | Display | |
| Data in CIF | 9d8d_validation.cif.gz | 58.2 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/9d8d ftp://data.pdbj.org/pub/pdb/validation_reports/d8/9d8d | HTTPS FTP |
-Related structure data
| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| 2 | ![]()
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| 3 | ![]()
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| 4 | ![]()
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| Unit cell |
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Components
| #1: Protein | Mass: 29220.473 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-GCP / #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | 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: 2.24 Å3/Da / Density % sol: 45.19 % |
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 26 % (w/v) PEG 4000, 0.2 M ammonium acetate, 0.1 M bicine (pH 8.4), 0.010 M magnesium chloride, 0.003 M GMPPCP |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97936 Å |
| Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2024 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.97936 Å / Relative weight: 1 |
| Reflection | Resolution: 2.11→88.99 Å / Num. obs: 57054 / % possible obs: 97.6 % / Redundancy: 1.8 % / CC1/2: 0.99 / Net I/σ(I): 9.4 |
| Reflection shell | Resolution: 2.11→2.15 Å / Num. unique obs: 5091 / CC1/2: 0.557 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→31.81 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.17 / Stereochemistry target values: ML
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.11→31.81 Å
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| Refine LS restraints |
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| LS refinement shell |
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| Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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| Refinement TLS group |
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About Yorodumi




X-RAY DIFFRACTION
United States, 2items
Citation
PDBj








