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Yorodumi- PDB-5ggy: X-ray crystal structure of Periplasmic Desferal binding protein F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ggy | ||||||
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Title | X-ray crystal structure of Periplasmic Desferal binding protein FhuD from Vibrio cholerae | ||||||
Components | Iron(III) ABC transporter, periplasmic iron-compound-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / Vibrio cholerae / Ferric siderophore binding protein / ABC transporter / Periplasmic / Desferal / apo-FhuD | ||||||
Function / homology | : / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Iron(III) ABC transporter, periplasmic iron-compound-binding protein Function and homology information | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Agarwal, S. / Dey, S. / Ghosh, B. / Dasgupta, J. | ||||||
Funding support | India, 1items
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Citation | Journal: To be published Title: X-ray crystal structure of Periplasmic Desferal binding protein FhuD from Vibrio cholerae Authors: Agarwal, S. / Biswas, M. / Dasgupta, J. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015 Title: Purification, crystallization and preliminary X-ray analysis of the periplasmic haem-binding protein HutB from Vibrio cholerae. Authors: Agarwal, S. / Biswas, M. / Dasgupta, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ggy.cif.gz | 219 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ggy.ent.gz | 174.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ggy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ggy_validation.pdf.gz | 439.5 KB | Display | wwPDB validaton report |
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Full document | 5ggy_full_validation.pdf.gz | 444.5 KB | Display | |
Data in XML | 5ggy_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 5ggy_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/5ggy ftp://data.pdbj.org/pub/pdb/validation_reports/gg/5ggy | HTTPS FTP |
-Related structure data
Related structure data | 1efdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31208.615 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 55-319 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae / Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: VC0395_A2582 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0A0H3AJ03 #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: 2.07 Å3/Da / Density % sol: 40.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 18%(w/v) PEG 6000, 0.1 M MES (pH 6.0), 0.1M Tris (pH 7) PH range: 6-7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.98 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.32 Å / Num. obs: 18616 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.5→2.6 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EFD Resolution: 2.5→47.316 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.23 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→47.316 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.7567 Å / Origin y: 60.0023 Å / Origin z: 13.7835 Å
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Refinement TLS group | Selection details: all |