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Yorodumi- PDB-5ggx: Crystal Structure of Fe3+ - Desferal bound siderophore binding pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ggx | ||||||
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Title | Crystal Structure of Fe3+ - Desferal bound siderophore binding protein FhuD from Vibrio cholerae | ||||||
Components | Iron(III) ABC transporter, periplasmic iron-compound-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / Vibrio cholerae / periplasmic protein / desferal / iron-Siderophore / ABC transporter / 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 / DEFEROXAMINE MESYLATE FE(III) COMPLEX / 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: 3.4 Å | ||||||
Authors | Agarwal, S. / Dey, S. / Ghosh, B. / Dasgupta, J. | ||||||
Funding support | India, 1items
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Citation | Journal: To be published Title: Crystal Structure of Fe3+ - Desferal bound siderophore 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 | 5ggx.cif.gz | 426.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ggx.ent.gz | 353.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ggx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ggx_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 5ggx_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 5ggx_validation.xml.gz | 42.5 KB | Display | |
Data in CIF | 5ggx_validation.cif.gz | 53.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/5ggx ftp://data.pdbj.org/pub/pdb/validation_reports/gg/5ggx | 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.: 4 / Fragment: UNP RESIDUES 55-319 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / 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 | ChemComp-DEF / |
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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: 5.46 Å3/Da / Density % sol: 77.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.8M ammonium sulfate, 0.1M HEPES (pH 7.0), 0.1M Tris (pH 7.0) |
-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 10, 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: 3.4→47.79 Å / Num. obs: 37750 / % possible obs: 100 % / Redundancy: 11.2 % / Net I/σ(I): 10 |
Reflection shell | Resolution: 3.4→3.55 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EFD Resolution: 3.4→43.055 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.11 / 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: 3.4→43.055 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: 110.8917 Å / Origin y: -30.6951 Å / Origin z: 6.6762 Å
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Refinement TLS group | Selection details: all |