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Yorodumi- PDB-4wvb: Crystal structure of GH63 mannosylglycerate hydrolase from Thermu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wvb | ||||||
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Title | Crystal structure of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with glucose | ||||||
Components | Uncharacterized protein | ||||||
Keywords | HYDROLASE / GH63 / (alpha/alpha)6-barrel | ||||||
Function / homology | Function and homology information trehalose metabolic process / alpha,alpha-trehalase activity / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Miyazaki, T. / Ichikawa, M. / Nishikawa, A. / Tonozuka, T. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2015 Title: Crystal structure and substrate-binding mode of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8. Authors: Miyazaki, T. / Ichikawa, M. / Iino, H. / Nishikawa, A. / Tonozuka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wvb.cif.gz | 188.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wvb.ent.gz | 148.7 KB | Display | PDB format |
PDBx/mmJSON format | 4wvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/4wvb ftp://data.pdbj.org/pub/pdb/validation_reports/wv/4wvb | HTTPS FTP |
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-Related structure data
Related structure data | 4wvaC 4wvcC 2z07S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 48839.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA0978 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJN0 #2: Chemical | #3: Chemical | ChemComp-MPD / ( #4: Sugar | ChemComp-GLC / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 30% MPD, 100 mM sodium citrate buffer, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. obs: 80188 / % possible obs: 99.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 51.3 |
Reflection shell | Resolution: 1.77→1.83 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 10.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z07 Resolution: 1.77→29.74 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.105 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.11 Å2
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Refinement step | Cycle: 1 / Resolution: 1.77→29.74 Å
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Refine LS restraints |
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