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- PDB-7b1z: Virulence-associated protein VapB from the intracellular pathogen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7b1z | ||||||
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Title | Virulence-associated protein VapB from the intracellular pathogen Rhodococcus equi | ||||||
![]() | Virulence associated protein VapB | ||||||
![]() | TOXIN / BETA BARREL / CONFORMATIONAL CHANGE / LIGAND BINDING SITE / VIRULENCE FACTOR | ||||||
Function / homology | Rhodococcus equi virulence-associated protein / Rhodococcus equi virulence-associated superfamily / Rhodococcus equi virulence-associated protein / NITRATE ION / Virulence associated protein VapB![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Geerds, C. / Niemann, H.H. | ||||||
![]() | ![]() Title: Conformational changes of loops highlight a potential binding site in Rhodococcus equi VapB. Authors: Geerds, C. / Haas, A. / Niemann, H.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 167.9 KB | Display | ![]() |
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PDB format | ![]() | 112.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 322.3 KB | Display | ![]() |
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Full document | ![]() | 323.2 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cv7S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12091.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Obtained by proteolytic digestion with proteinase K. N- and C-terminus are not defined with certainty. Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.53 % / Description: plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 14% PEG 4000, 0.2 M Mg(NO3)2; protein concentration: 10 mg/ml; protein buffer: 25 mM Tris, pH 7.0, 20 mM NaCl; drop size and ratio: 1 ul protein + 0.5 ul reservoir |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23953 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→50 Å / Num. obs: 25467 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 1 / Rrim(I) all: 0.039 / Net I/σ(I): 28.74 |
Reflection shell | Resolution: 1.71→1.75 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1845 / CC1/2: 0.85 / Rrim(I) all: 0.657 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4CV7 Resolution: 1.71→42.93 Å / SU ML: 0.1844 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.6568 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→42.93 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 86 - 194 / Label seq-ID: 1 - 109
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