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Yorodumi- PDB-4re4: Different transition state conformations for the hydrolysis of be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4re4 | ||||||
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Title | Different transition state conformations for the hydrolysis of beta-mannosides and beta-glucosides in the rice Os7BGlu26 family GH1 beta-mannosidase/beta-glucosidase | ||||||
Components | Beta-mannosidase/beta-glucosidase | ||||||
Keywords | HYDROLASE / GH1 | ||||||
Function / homology | Function and homology information beta-mannosidase / beta-D-fucosidase activity / beta-mannosidase activity / beta-glucosidase activity / beta-galactosidase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Oryza sativa Indica Group (long-grained rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Tankrathok, A. / Iglesias-Fernandez, J. / Williams, R.J. / Hakki, Z. / Robinson, R.C. / Hrmova, M. / Rovira, C. / Williams, S.J. / Ketudat Cairns, J.R. | ||||||
Citation | Journal: ACS CATALYSIS / Year: 2015 Title: A Single Glycosidase Harnesses Different Pyranoside Ring Transition State Conformations for Hydrolysis of Mannosides and Glucosides Authors: Tankrathok, A. / Iglesias-Fernandez, J. / Williams, R.J. / Pengthaisong, S. / Baiya, S. / Hakki, Z. / Robinson, R.C. / Hrmova, M. / Rovira, C. / Williams, S.J. / Ketudat Cairns, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4re4.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4re4.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 4re4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/4re4 ftp://data.pdbj.org/pub/pdb/validation_reports/re/4re4 | HTTPS FTP |
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-Related structure data
Related structure data | 4re2C 4re3C 4jhoS 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: 57703.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Indica Group (long-grained rice) Plasmid: pET32A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettagami DE3 References: UniProt: B5ABY0, UniProt: A2YPH1*PLUS, beta-mannosidase | ||||
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#2: Chemical | ChemComp-IFM / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EPE / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.57 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.25 Details: 0.8M K/Na tartrate, 0.1M Na HEPES, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→30 Å / Num. all: 30667 / Num. obs: 30667 / % possible obs: 99.9 % / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JHO Resolution: 2.29→28.84 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 22.354 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→28.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.293→2.352 Å / Total num. of bins used: 20
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