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Yorodumi- PDB-4mst: Crystal Structure of a putative catalytic domain of a chitinase-l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mst | ||||||
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Title | Crystal Structure of a putative catalytic domain of a chitinase-like protein (HbCLP1) from Hevea brasiliensis | ||||||
Components | class I chitinase | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin / chitinase-like protein / all alpha / extracellular / hydrolase-like protein / inactive chitinase | ||||||
Function / homology | Function and homology information chitin catabolic process / chitin binding / defense response to fungus / cell wall macromolecule catabolic process / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Hevea brasiliensis (rubber tree) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.927 Å | ||||||
Authors | Martinez-Caballero, S. / Hermoso, J.A. / Rodriguez-Romero, A. | ||||||
Citation | Journal: Febs J. / Year: 2014 Title: Comparative study of two GH19 chitinase-like proteins from Hevea brasiliensis, one exhibiting a novel carbohydrate-binding domain. Authors: Martinez-Caballero, S. / Cano-Sanchez, P. / Mares-Mejia, I. / Diaz-Sanchez, A.G. / Macias-Rubalcava, M.L. / Hermoso, J.A. / Rodriguez-Romero, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mst.cif.gz | 111.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mst.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 4mst.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mst_validation.pdf.gz | 414 KB | Display | wwPDB validaton report |
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Full document | 4mst_full_validation.pdf.gz | 413.9 KB | Display | |
Data in XML | 4mst_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 4mst_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/4mst ftp://data.pdbj.org/pub/pdb/validation_reports/ms/4mst | HTTPS FTP |
-Related structure data
Related structure data | 4mpiC 3cqlS C: citing same article (ref.) 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: 26554.670 Da / Num. of mol.: 2 Fragment: putative catalytic domain (pCatD, UNP residues 54-295) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Strain: RIMM600 / Gene: Hbchi-L1, rq30 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami DE3 pLysS / References: UniProt: Q949H3, chitinase #2: Chemical | #3: 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: 2.34 Å3/Da / Density % sol: 47.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 7 mg/mL protein, 0.1 M Tris-HCl, pH 8.3, 0.2 M magnesium chloride, 30% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97857 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.927→83.316 Å / Num. all: 37792 / Num. obs: 37443 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 22.22 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 14.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CQL Resolution: 1.927→41.658 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 20.05 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.927→41.658 Å
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Refine LS restraints |
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LS refinement shell |
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