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Yorodumi- PDB-4nz1: Structure of Vibrio cholerae chitin de-N-acetylase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nz1 | |||||||||
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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 | |||||||||
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: 2.051 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 | 4nz1.cif.gz | 188.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nz1.ent.gz | 145.6 KB | Display | PDB format |
PDBx/mmJSON format | 4nz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nz1_validation.pdf.gz | 814.2 KB | Display | wwPDB validaton report |
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Full document | 4nz1_full_validation.pdf.gz | 816.6 KB | Display | |
Data in XML | 4nz1_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 4nz1_validation.cif.gz | 54.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/4nz1 ftp://data.pdbj.org/pub/pdb/validation_reports/nz/4nz1 | HTTPS FTP |
-Related structure data
Related structure data | 4ny2SC 4nyuC 4nyyC 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
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 46895.910 Da / Num. of mol.: 2 / 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 #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 5 types, 665 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | #7: 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: 2.33 Å3/Da / Density % sol: 47.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris pH 8.5, 0.2M CaCl2, 20% (w/v) PEG 4000, 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2012 |
Radiation | Monochromator: 0.9537 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→29.055 Å / Num. obs: 53316 / % possible obs: 99.27 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 20.46 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.91 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 1.86 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.02 / Num. unique all: 16089 / % possible all: 94.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NY2 Resolution: 2.051→29.05 Å / SU ML: 0.21 / σ(F): 2.02 / Phase error: 18.73 / 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: 2.051→29.05 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: 19
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