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Yorodumi- PDB-4rl3: Crystal Structure of the Catalytic Domain of a family GH18 Chitin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rl3 | ||||||
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Title | Crystal Structure of the Catalytic Domain of a family GH18 Chitinase from fern, Peteris ryukyuensis | ||||||
Components | Chitinase AChitinase A N-terminal domain | ||||||
Keywords | HYDROLASE / Chitinase / Carbohydrate | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Pteris ryukyuensis (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Umemoto, N. / Numata, T. / Ohnuma, T. / Fukamizo, T. | ||||||
Citation | Journal: Planta / Year: 2015 Title: A class III chitinase without disulfide bonds from the fern, Pteris ryukyuensis: crystal structure and ligand-binding studies. Authors: Kitaoku, Y. / Umemoto, N. / Ohnuma, T. / Numata, T. / Taira, T. / Sakuda, S. / Fukamizo, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rl3.cif.gz | 124.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rl3.ent.gz | 95.1 KB | Display | PDB format |
PDBx/mmJSON format | 4rl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/4rl3 ftp://data.pdbj.org/pub/pdb/validation_reports/rl/4rl3 | HTTPS FTP |
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-Related structure data
Related structure data | 3simS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28772.982 Da / Num. of mol.: 2 / Fragment: Catalytic Domain (UNP RESIDIES 153-423) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pteris ryukyuensis (plant) / Gene: prchiA / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0WYK2, chitinase #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | #5: 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: 2.25 Å3/Da / Density % sol: 45.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 0.2M Magnesium acetate tetrahydrate, 20% w/v Polyethylene glycol 3350, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 22, 2012 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator, luqid nitrogen cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→71.17 Å / Num. obs: 70282 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 68.92 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 32.86 / Num. unique all: 20606 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SIM Resolution: 1.57→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.063 / SU ML: 0.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.07 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.963 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.57→1.611 Å / Total num. of bins used: 20
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