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- PDB-3act: Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase H... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3act | ||||||
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Title | Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase Histidine mutant | ||||||
![]() | Cellobiose Phosphorylase | ||||||
![]() | TRANSFERASE / beta-sandwich / (alpha/alpha)6 barrel / phosphorylase / glycoside hydrolase family 94 | ||||||
Function / homology | ![]() glycosyltransferase activity / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hidaka, M. / Hayashi, M.A. / Fushinobu, S. | ||||||
![]() | ![]() Title: Engineering of cellobiose phosphorylase Authors: Arai, T. / Hayashi, M.A. / Hidaka, M. / Kitaoka, M. / Wakagi, T. / Shoun, H. / Fushinobu, S. #1: ![]() Title: Structural dissection of the reaction mechanism of cellobiose phosphorylase Authors: Hidaka, M. / Kitaoka, M. / Hayashi, K. / Wakagi, T. / Shoun, H. / Fushinobu, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 383.4 KB | Display | ![]() |
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PDB format | ![]() | 300.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.3 KB | Display | ![]() |
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Full document | ![]() | 498.2 KB | Display | |
Data in XML | ![]() | 78.8 KB | Display | |
Data in CIF | ![]() | 125.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3acsC ![]() 3afjC ![]() 2cqtS 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 4 molecules AB![](data/chem/img/BGC.gif)
![](data/chem/img/BGC.gif)
#1: Protein | Mass: 93047.758 Da / Num. of mol.: 2 / Mutation: H666N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | |
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-Non-polymers , 4 types, 2211 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/K.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: Na/K phosphate, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 25, 2008 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 141447 / % possible obs: 97.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.86 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CQT Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.256 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.268 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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