+Open data
-Basic information
Entry | Database: PDB / ID: 2dvz | ||||||
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Title | Structure of a periplasmic transporter | ||||||
Components | Putative exported protein | ||||||
Keywords | TRANSPORT PROTEIN / periplamsic binding proteins / carboxylate binding / glutamate / Bordetella | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bordetella pertussis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Huvent, I. / Belrhali, H. / Antoine, R. / Bompard, C. / Locht, C. / Jacob-Dubuisson, F. / Villeret, V. | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006 Title: Structural analysis of Bordetella pertussis BugE solute receptor in a bound conformation Authors: Huvent, I. / Belrhali, H. / Antoine, R. / Bompard, C. / Locht, C. / Jacob-Dubuisson, F. / Villeret, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dvz.cif.gz | 127 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dvz.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/2dvz ftp://data.pdbj.org/pub/pdb/validation_reports/dv/2dvz | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-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: 33942.410 Da / Num. of mol.: 1 / Fragment: residues 13-314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis (bacteria) / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q7W0A0 | ||||
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#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-GLU / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.3 Details: 0.1M CdCl2, 0.1M sodium acetate, 30-32% (v/v) PEG 400 or 34-40% (v/v) PEG 200, pH 4.30, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9758 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9758 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→15 Å / Num. obs: 15977 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 9 % / Rsym value: 0.079 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.125 / % possible all: 72 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.885 / SU B: 12.912 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.349 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.358 Å / Total num. of bins used: 20
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