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Open data
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Basic information
Entry | Database: PDB / ID: 2dvz | ||||||
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Title | Structure of a periplasmic transporter | ||||||
![]() | Putative exported protein | ||||||
![]() | TRANSPORT PROTEIN / periplamsic binding proteins / carboxylate binding / glutamate / Bordetella | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huvent, I. / Belrhali, H. / Antoine, R. / Bompard, C. / Locht, C. / Jacob-Dubuisson, F. / Villeret, V. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127 KB | Display | ![]() |
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PDB format | ![]() | 105.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.1 KB | Display | ![]() |
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Full document | ![]() | 444.3 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 21.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-GLU / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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