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Yorodumi- PDB-4oui: Structure of Vibrio cholerae chitin de-N-acetylase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oui | |||||||||
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Title | Structure of Vibrio cholerae chitin de-N-acetylase in complex with TRIACETYLCHITOTRIOSE (CTO) | |||||||||
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: 2.17 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 | 4oui.cif.gz | 192.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oui.ent.gz | 148.7 KB | Display | PDB format |
PDBx/mmJSON format | 4oui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oui_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4oui_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4oui_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 4oui_validation.cif.gz | 56.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/4oui ftp://data.pdbj.org/pub/pdb/validation_reports/ou/4oui | HTTPS FTP |
-Related structure data
Related structure data | 4ny2C 4nyuC 4nyyC 4nz1C 4nz3C 4nz4SC 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
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 46895.910 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 23-427 / Mutation: D39S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VCNHCC010F_001593 / Production host: Escherichia coli (E. coli) / References: UniProt: M7M1G8, chitin deacetylase #2: Polysaccharide | |
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-Non-polymers , 4 types, 726 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: 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: 2.61 Å3/Da / Density % sol: 52.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M MgCl2, 0.1M TRIS pH 8.5, 17% (w/v) PEG 20000, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2013 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→83.32 Å / Num. all: 52387 / Num. obs: 52387 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 11.925 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.17→2.23 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3589 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NZ4 Resolution: 2.17→83.32 Å / SU ML: 0.24 / σ(F): 0.14 / Phase error: 21.68 / 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: 2.17→83.32 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: 30
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