+Open data
-Basic information
Entry | Database: PDB / ID: 3hbd | ||||||
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Title | Class IV chitinase structure from Picea abies at 1.8A | ||||||
Components | Class IV chitinase Chia4-Pa2 | ||||||
Keywords | HYDROLASE / endochitinase / chitinase / class IV / family 19 / conformational changes / Chitin-binding / Glycosidase | ||||||
Function / homology | Function and homology information chitinase / chitinase activity / chitin catabolic process / chitin binding / cell wall macromolecule catabolic process / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Picea abies (Norway spruce) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ubhayasekera, W. / Mowbray, S.L. | ||||||
Citation | Journal: Plant Mol.Biol. / Year: 2009 Title: The first crystal structures of a family 19 class IV chitinase: the enzyme from Norway spruce. Authors: Ubhayasekera, W. / Rawat, R. / Ho, S.W. / Wiweger, M. / Von Arnold, S. / Chye, M.L. / Mowbray, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hbd.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hbd.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 3hbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hbd_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
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Full document | 3hbd_full_validation.pdf.gz | 445.6 KB | Display | |
Data in XML | 3hbd_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 3hbd_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/3hbd ftp://data.pdbj.org/pub/pdb/validation_reports/hb/3hbd | HTTPS FTP |
-Related structure data
Related structure data | 3hbeC 3hbhC 1cnsS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21531.814 Da / Num. of mol.: 1 / Fragment: Catalytic module Source method: isolated from a genetically manipulated source Source: (gene. exp.) Picea abies (Norway spruce) / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / References: UniProt: Q6WSR8, chitinase | ||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.91 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% w/v polyethylene glycol 3000, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9998 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 14815 / % possible obs: 97.4 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.1 / % possible all: 88.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology model of the Picea abies chitinase built on barley seed chitinase (PDB entry 1CNS) Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.667 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.131 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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