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Yorodumi- PDB-3acs: Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3acs | ||||||
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Title | Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase W488F mutant | ||||||
Components | Cellobiose Phosphorylase | ||||||
Keywords | TRANSFERASE / beta-sandwich / (alpha/alpha)6 barrel / phosphorylase / glycoside hydrolase family 94 | ||||||
Function / homology | Function and homology information glycosyltransferase activity / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Cellvibrio gilvus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Hidaka, M. / Arai, T. / Fushinobu, S. | ||||||
Citation | Journal: To be Published Title: Engineering of cellobiose phosphorylase Authors: Arai, T. / Hayashi, M.A. / Hidaka, M. / Kitaoka, M. / Wakagi, T. / Shoun, H. / Fushinobu, S. #1: Journal: Biochem.J. / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3acs.cif.gz | 344.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3acs.ent.gz | 272.8 KB | Display | PDB format |
PDBx/mmJSON format | 3acs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3acs_validation.pdf.gz | 470.4 KB | Display | wwPDB validaton report |
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Full document | 3acs_full_validation.pdf.gz | 484.6 KB | Display | |
Data in XML | 3acs_validation.xml.gz | 63.5 KB | Display | |
Data in CIF | 3acs_validation.cif.gz | 92.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/3acs ftp://data.pdbj.org/pub/pdb/validation_reports/ac/3acs | HTTPS FTP |
-Related structure data
Related structure data | 3actC 3afjC 2cqsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 93032.766 Da / Num. of mol.: 2 / Mutation: W488F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellvibrio gilvus (bacteria) / Strain: ATCC13127 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66264, cellobiose phosphorylase #2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: ammonium sulfate, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2006 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 57216 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.89 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CQS Resolution: 2.51→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.926 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R Free: 0.272 / 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: 22.227 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.506→2.571 Å / Total num. of bins used: 20
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