+Open data
-Basic information
Entry | Database: PDB / ID: 7xmh | ||||||
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Title | Crystal structure of a rice class IIIb chitinase, Oschib2 | ||||||
Components | Putative class III chitinase | ||||||
Keywords | HYDROLASE / GH18 chitinase / family 8 pathogenesis-related protein | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Oryza sativa (Asian cultivated rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å | ||||||
Authors | Jun, T. / Tomoya, T. / Tomoyuki, N. / Takayuki, O. | ||||||
Funding support | 1items
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Citation | Journal: Plant Sci. / Year: 2023 Title: Characterization of two rice GH18 chitinases belonging to family 8 of plant pathogenesis-related proteins. Authors: Tanaka, J. / Takashima, T. / Abe, N. / Fukamizo, T. / Numata, T. / Ohnuma, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xmh.cif.gz | 82.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xmh.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 7xmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xmh_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 7xmh_full_validation.pdf.gz | 447.9 KB | Display | |
Data in XML | 7xmh_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 7xmh_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/7xmh ftp://data.pdbj.org/pub/pdb/validation_reports/xm/7xmh | HTTPS FTP |
-Related structure data
Related structure data | 4rl3S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32062.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: OSJNBa0061K21.7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8S870 | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: Sodium acetate trihydrate pH 4.5, 3.0 M Sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→46.72 Å / Num. obs: 101845 / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 32.49 |
Reflection shell | Resolution: 1.18→1.2 Å / Rmerge(I) obs: 0.167 / Num. unique obs: 4567 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RL3 Resolution: 1.18→46.72 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.374 / SU ML: 0.018 / Cross valid method: NONE / ESU R: 0.033 / ESU R Free: 0.033 Details: Hydrogens have been added in their 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: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.561 Å2
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Refinement step | Cycle: LAST / Resolution: 1.18→46.72 Å
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Refine LS restraints |
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LS refinement shell |
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