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Yorodumi- PDB-7w8f: Crystal structure of siderophore binding protein VatD from Vibrio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w8f | ||||||
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Title | Crystal structure of siderophore binding protein VatD from Vibrio vulnificus M2799 complexed with Desferal | ||||||
Components | Putative periplasm binding protein | ||||||
Keywords | METAL BINDING PROTEIN / periplasmic iron-compound binding protein / Deferoxamine complex | ||||||
Function / homology | ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / : / desferrioxamine B / Putative periplasm binding protein Function and homology information | ||||||
Biological species | Vibrio vulnificus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Tomoo, K. / Miyamoto, K. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of siderophore binding protein VatD from Vibrio vulnificus M2799 complexed with Desferal Authors: Tomoo, K. / Miyamoto, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w8f.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w8f.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 7w8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/7w8f ftp://data.pdbj.org/pub/pdb/validation_reports/w8/7w8f | HTTPS FTP |
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-Related structure data
Related structure data | 1efdS 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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Unit cell |
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-Components
#1: Protein | Mass: 31094.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: fhuD / Production host: Escherichia coli (E. coli) / References: UniProt: Q845T3 | ||||||
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#2: Chemical | ChemComp-KTY / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30%(w/v) PEG-3,350, 50mM MgCl2, 0.1M Bis-Tris pH6.5 |
-Data collection
Diffraction | Mean temperature: 130 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→26.3 Å / Num. obs: 20814 / % possible obs: 97.6 % / Redundancy: 3.48 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.345 / Num. unique obs: 2172 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EFD Resolution: 1.9→26.103 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.163 / SU B: 4.007 / SU ML: 0.115 / Average fsc free: 0.9181 / Average fsc work: 0.9315 / Cross valid method: FREE R-VALUE / ESU R: 0.179 / ESU R Free: 0.154 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.187 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→26.103 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: 20
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