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Yorodumi- PDB-4nyu: Structure of Vibrio cholerae chitin de-N-acetylase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nyu | ||||||
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Title | Structure of Vibrio cholerae chitin de-N-acetylase in complex with acetate ion (ACT) in C 2 2 21 | ||||||
Components | Deacetylase DA1 | ||||||
Keywords | HYDROLASE / (beta/alpha)7 / carbohydrate esterase | ||||||
Function / homology | Function and homology information Seminal Fluid Protein PDC-109 (Domain B) - #90 / Glycoside hydrolase/deacetylase / Seminal Fluid Protein PDC-109 (Domain B) / Ribbon / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Albesa-Jove, D. / Andres, E. / Biarnes, X. / Planas, A. / Guerin, M.E. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Structural basis of chitin oligosaccharide deacetylation. Authors: Andres, E. / Albesa-Jove, D. / Biarnes, X. / Moerschbacher, B.M. / Guerin, M.E. / Planas, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nyu.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nyu.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 4nyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nyu_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
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Full document | 4nyu_full_validation.pdf.gz | 454.2 KB | Display | |
Data in XML | 4nyu_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 4nyu_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/4nyu ftp://data.pdbj.org/pub/pdb/validation_reports/ny/4nyu | HTTPS FTP |
-Related structure data
Related structure data | 4ny2SC 4nyyC 4nz1C 4nz3C 4nz4C 4ouiC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46923.922 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 23-427 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: deaA, VCNHCC010F_001593 / Production host: Escherichia coli (E. coli) / References: UniProt: M7M1G8, chitin deacetylase |
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-Non-polymers , 5 types, 437 molecules
#2: Chemical | ChemComp-ZN / | ||
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#3: Chemical | ChemComp-CA / | ||
#4: Chemical | ChemComp-ACT / | ||
#5: Chemical | ChemComp-GOL / #6: 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: 2.31 Å3/Da / Density % sol: 46.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M sodium cacodylate, 0.2M Ca(OAc)2 and 18% (w/v) PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2012 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→100 Å / Num. all: 27231 / Num. obs: 27231 / % possible obs: 95.58 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 20.87 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.11 |
Reflection shell | Resolution: 2.03→2.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.35 / Num. unique all: 2169 / % possible all: 80.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NY2 Resolution: 2.03→46.868 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 22.61 / 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: 2.03→46.868 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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