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Yorodumi- PDB-5ylg: Crystal Structure of LysM domain from pteris ryukyuensis chitinase A -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ylg | ||||||
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Title | Crystal Structure of LysM domain from pteris ryukyuensis chitinase A | ||||||
Components | Chitinase AChitinase A N-terminal domain | ||||||
Keywords | SUGAR BINDING PROTEIN / CBM / Chitinase / LysM / PLANT PROTEIN | ||||||
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: 1.48 Å | ||||||
Authors | Ohnuma, T. / Kitaoku, Y. / Umemoto, N. / Numata, T. / Fukamizo, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of LysM domain from pteris ryukyuensis chitinase A Authors: Kitaoku, Y. / Umemoto, N. / Taira, T. / 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 | 5ylg.cif.gz | 55.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ylg.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ylg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/5ylg ftp://data.pdbj.org/pub/pdb/validation_reports/yl/5ylg | HTTPS FTP |
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-Related structure data
Related structure data | 4pxvSC 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5295.958 Da / Num. of mol.: 4 / Fragment: LysM domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pteris ryukyuensis (plant) / Gene: prchiA / Production host: Escherichia coli (E. coli) / References: UniProt: Q0WYK2 #2: Chemical | #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: 2.12 Å3/Da / Density % sol: 42.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.05 M Zinc acetate dihydrate, 25% PEG 3350, 20% glycerol |
-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 315r / Detector: CCD / Date: Jun 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→50 Å / Num. obs: 30690 / % possible obs: 99.4 % / Redundancy: 10.6 % / Net I/σ(I): 57.6 |
Reflection shell | Resolution: 1.48→1.51 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 6.7 / Num. unique obs: 12086 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PXV Resolution: 1.48→46.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.155 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.078 / 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: 13.646 Å2
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Refinement step | Cycle: 1 / Resolution: 1.48→46.18 Å
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Refine LS restraints |
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