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Yorodumi- PDB-4mck: Crystal structure of Family GH19, Class IV chitinase from Zea mays -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mck | ||||||
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Title | Crystal structure of Family GH19, Class IV chitinase from Zea mays | ||||||
Components | Chitinase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information amino sugar metabolic process / endochitinase activity / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / defense response to fungus / cell wall macromolecule catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Chaudet, M.M. / Rose, D.R. | ||||||
Citation | Journal: Protein Sci. / Year: 2014 Title: Crystallographic structure of ChitA, a glycoside hydrolase family 19, plant class IV chitinase from Zea mays. Authors: Chaudet, M.M. / Naumann, T.A. / Price, N.P. / Rose, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mck.cif.gz | 59.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mck.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 4mck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mck_validation.pdf.gz | 418.9 KB | Display | wwPDB validaton report |
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Full document | 4mck_full_validation.pdf.gz | 431.1 KB | Display | |
Data in XML | 4mck_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4mck_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/4mck ftp://data.pdbj.org/pub/pdb/validation_reports/mc/4mck | HTTPS FTP |
-Related structure data
Related structure data | 3hbdS 4mcl S: Starting model for refinement |
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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: 22029.662 Da / Num. of mol.: 1 / Fragment: catalytic module (UNP residues 81-278) / Mutation: E62Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Strain: LH82 / Gene: chiA / Plasmid: pPICZ'alpha'A / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 References: UniProt: Q6JBL3, UniProt: P29022*PLUS, chitinase |
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#2: Water | ChemComp-HOH / |
Sequence details | THE AUTHORS HAVE VERIFIED THE PROTEIN SEQUENCE BIOCHEMICA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1.5 M ammonium sulfate, 0.1 M Tris, 0.16 M potassium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 12, 2012 |
Radiation | Monochromator: VariMax HF optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→48.416 Å / Num. obs: 28893 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 54.6 / Redundancy: 10.5 % / Biso Wilson estimate: 16.34 Å2 / Rmerge(I) obs: 0.044 |
Reflection shell | Highest resolution: 1.5 Å / Mean I/σ(I) obs: 3.3 / % possible all: 63.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HBD Resolution: 1.5→25.915 Å / SU ML: 0.1 / σ(F): 1.5 / Phase error: 20.25 / Stereochemistry target values: ML Details: FREE R WAS USED FOR CROSS-VALIDATION, BUT THE FREE R TEST SET WAS UNAVAILABLE AT THE TIME OF DEPOSITION.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→25.915 Å
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Refine LS restraints |
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LS refinement shell |
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