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- PDB-7o9p: Crystal structure of the Awp3b (adhesin-like wall protein 3b) A-d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o9p | ||||||
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Title | Crystal structure of the Awp3b (adhesin-like wall protein 3b) A-domain from Candida glabrata showing a gadolinium cluster | ||||||
![]() | AWP3b | ||||||
![]() | CELL ADHESION / Candida glabrata / adhesion / adhesin / Awp / adhesin-like wall protein / gadolinium / gadolinium cluster / lanthanide / lanthanide cluster / haze-protective factors / beta-helix | ||||||
Function / homology | GADOLINIUM ATOM / AWP3b![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Reithofer, V. / de Groot, P. / Essen, L.-O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A novel class of Candida glabrata cell wall proteins with beta-helix fold mediates adhesion in clinical isolates. Authors: Reithofer, V. / Fernandez-Pereira, J. / Alvarado, M. / de Groot, P. / Essen, L.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.5 KB | Display | ![]() |
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PDB format | ![]() | 64.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.5 KB | Display | ![]() |
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Full document | ![]() | 438.5 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 38713.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-GD / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.34 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium chloride, 0.1 M Tris pH 7.0, 3.0 M sodium chloride crystals soaked with 50 mM gadolinium (III) acetate |
-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: Jun 25, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.71237 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.99→84.2 Å / Num. obs: 30650 / % possible obs: 99.8 % / Redundancy: 18.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.025 / Rrim(I) all: 0.107 / Net I/σ(I): 18.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.06 Å2 / Biso mean: 32.892 Å2 / Biso min: 16.47 Å2
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Refinement step | Cycle: final / Resolution: 1.99→27.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.04 Å / Rfactor Rfree error: 0
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