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Yorodumi- PDB-4nz3: Structure of Vibrio cholerae chitin de-N-acetylase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nz3 | |||||||||
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Title | Structure of Vibrio cholerae chitin de-N-acetylase in complex with DI(N-ACETYL-D-GLUCOSAMINE) (CBS) in P 21 21 21 | |||||||||
Components | Deacetylase DA1 | |||||||||
Keywords | HYDROLASE / (beta/alpha)7 / carbohydrate esterase | |||||||||
Function / homology | 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 / : Function and homology information | |||||||||
Biological species | Vibrio cholerae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.114 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 | 4nz3.cif.gz | 195.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nz3.ent.gz | 150.5 KB | Display | PDB format |
PDBx/mmJSON format | 4nz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/4nz3 ftp://data.pdbj.org/pub/pdb/validation_reports/nz/4nz3 | HTTPS FTP |
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-Related structure data
Related structure data | 4ny2SC 4nyuC 4nyyC 4nz1C 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
-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) / Production host: Escherichia coli (E. coli) / References: UniProt: M7M1G8, chitin deacetylase #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 859 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: 2.55 Å3/Da / Density % sol: 51.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl pH 8.5, 0.1M MgCl2, 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: I04 / Wavelength: 0.9537 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 20, 2012 |
Radiation | Monochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→29.711 Å / Num. obs: 54749 / % possible obs: 96.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 17.97 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 7.77 |
Reflection shell | Resolution: 2.11→2.19 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.82 / Num. unique all: 15366 / % possible all: 86.28 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NY2 Resolution: 2.114→29.711 Å / SU ML: 0.23 / σ(F): 2.02 / Phase error: 18.11 / 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: 2.114→29.711 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: 20
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