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- PDB-4cvu: Structure of Fungal beta-mannosidase from Glycoside Hydrolase Fam... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cvu | |||||||||||||||
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Title | Structure of Fungal beta-mannosidase from Glycoside Hydrolase Family 2 of Trichoderma harzianum | |||||||||||||||
![]() | BETA-MANNOSIDASE | |||||||||||||||
![]() | HYDROLASE | |||||||||||||||
Function / homology | ![]() beta-mannosidase / beta-mannosidase activity / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Muniz, J.R.C. / Aparicio, R. / Santos, J.C. / Nascimento, A.S. / Golubev, A.M. / Polikarpov, I. | |||||||||||||||
![]() | ![]() Title: Insights into the structure and function of fungal beta-mannosidases from glycoside hydrolase family 2 based on multiple crystal structures of the Trichoderma harzianum enzyme. Authors: Nascimento, A.S. / Muniz, J.R. / Aparicio, R. / Golubev, A.M. / Polikarpov, I. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 392.9 KB | Display | ![]() |
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PDB format | ![]() | 324.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 43.7 KB | Display | |
Data in CIF | ![]() | 66.3 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 105480.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 5 types, 11 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(2-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(2-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 7 types, 768 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-CD / #8: Chemical | ChemComp-NA / #9: Chemical | ChemComp-PG4 / | #10: Chemical | ChemComp-PEG / | #11: Chemical | ChemComp-CA / | #12: Chemical | ChemComp-CL / | #13: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70.12 % / Description: NONE |
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Crystal grow | Details: 26% PEG 400, 0.13 M CDCL2, 0.1 M SODIUM ACETATE PH 4.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.545 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.3 Å / Num. obs: 131814 / % possible obs: 99.1 % / Observed criterion σ(I): 1.7 / Redundancy: 7.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.34 / Mean I/σ(I) obs: 1.7 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.9→117.7 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.971 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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 mean: 46.084 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→117.7 Å
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Refine LS restraints |
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