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- PDB-5a7v: The GH130 family of mannoside phosphorylases contains glycoside h... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a7v | ||||||
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Title | The GH130 family of mannoside phosphorylases contains glycoside hydrolases that target beta-1,2 mannosidic linkages in Candida mannan | ||||||
![]() | (PUTATIVE GLYCOSIDASE PH117- ...) x 2 | ||||||
![]() | HYDROLASE / GLYCOSIDE HYDROLASE / PHOSPHORYLASE / CELL WALL / YEAST | ||||||
Function / homology | ![]() hydrolase activity, acting on glycosyl bonds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cuskin, F. / Basle, A. / Day, A.M. / Ladeveze, S. / Potocki-Veronese, G. / Davies, G.J. / Gilbert, H.J. / Lowe, E. | ||||||
![]() | ![]() Title: The Gh130 Family of Mannoside Phosphorylases Contains Glycoside Hydrolases that Target Beta-1,2 Mannosidic Linkages in Candida Mannan Authors: Cuskin, F. / Basle, A. / Day, A.M. / Ladeveze, S. / Potocki-Veronese, G. / Davies, G.J. / Gilbert, H.J. / Lowe, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 340.8 KB | Display | ![]() |
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PDB format | ![]() | 278.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 489 KB | Display | ![]() |
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Full document | ![]() | 495 KB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 57.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qc2S 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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1 | ![]()
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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
-PUTATIVE GLYCOSIDASE PH117- ... , 2 types, 2 molecules AB
#1: Protein | Mass: 43425.648 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-383 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#2: Protein | Mass: 43471.734 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-383 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
-Sugars , 2 types, 6 molecules ![](data/chem/img/BMA.gif)
![](data/chem/img/MAN.gif)
![](data/chem/img/MAN.gif)
#3: Sugar | #4: Sugar | ChemComp-MAN / |
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-Non-polymers , 2 types, 867 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63 % / Description: NONE |
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Crystal grow | Details: 2.2 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→46.58 Å / Num. obs: 243880 / % possible obs: 98.3 % / Observed criterion σ(I): 1.8 / Redundancy: 3.4 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.8 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3QC2 Resolution: 1.35→118.11 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.38 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-16 IN CHAIN A AND 1-25 IN CHAIN B ARE DISORDERED DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→118.11 Å
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Refine LS restraints |
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