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Open data
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Basic information
Entry | Database: PDB / ID: 7d2a | ||||||
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Title | CBM32 of AlyQ in complex with 4,5-unsaturated mannuronic acid | ||||||
![]() | AlyQ | ||||||
![]() | SUGAR BINDING PROTEIN / CBM32 / alginate | ||||||
Function / homology | ![]() hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Teh, A.H. / Sim, P.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for binding uronic acids by family 32 carbohydrate-binding modules. Authors: Teh, A.H. / Sim, P.F. / Hisano, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.7 KB | Display | ![]() |
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PDB format | ![]() | 29.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7d29C ![]() 5xnrS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 16095.180 Da / Num. of mol.: 1 / Fragment: CBM32 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 163 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / |
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#4: Chemical | ChemComp-PG4 / |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M sodium HEPES, 2% PEG 400, 2.0M ammonium sulphate, 10mg/ml enzymatically degraded sodium alginate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→40.34 Å / Num. obs: 18779 / % possible obs: 91.5 % / Redundancy: 6.73 % / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.046 / Χ2: 0.95 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.57→1.63 Å / Redundancy: 5.97 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 6.9 / Num. unique obs: 1284 / Rrim(I) all: 0.223 / Χ2: 1.19 / % possible all: 63.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XNR Resolution: 1.57→40.34 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.107 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.083
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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 BULK SOLVENT | ||||||||||||||||||||
Displacement parameters | Biso mean: 14.486 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→40.34 Å
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LS refinement shell | Resolution: 1.57→1.611 Å
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