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Yorodumi- PDB-2vzt: Complex of Amycolatopsis orientalis exo-chitosanase CsxA E541A wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vzt | |||||||||
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Title | Complex of Amycolatopsis orientalis exo-chitosanase CsxA E541A with PNP-beta-D-glucosamine | |||||||||
Components | EXO-BETA-D-GLUCOSAMINIDASE | |||||||||
Keywords | HYDROLASE / GH2 / CSXA / PNP-GLUCOSAMINE / GLYCOSIDE HYDROLASE / EXO-BETA-D-GLUCOSAMINIDASE | |||||||||
Function / homology | Function and homology information exo-1,4-beta-D-glucosaminidase / exo-1,4-beta-D-glucosaminidase activity / chitin catabolic process / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region Similarity search - Function | |||||||||
Biological species | AMYCOLATOPSIS ORIENTALIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å | |||||||||
Authors | Lammerts van Bueren, A. / Ghinet, M.G. / Gregg, K. / Fleury, A. / Brzezinski, R. / Boraston, A.B. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: The Structural Basis of Substrate Recognition in an Exo-Beta-D-Glucosaminidase Involved in Chitosan Hydrolysis. Authors: Lammerts Van Bueren, A. / Ghinet, M.G. / Gregg, K. / Fleury, A. / Brzezinski, R. / Boraston, A.B. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vzt.cif.gz | 350 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vzt.ent.gz | 280.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vzt_validation.pdf.gz | 988.1 KB | Display | wwPDB validaton report |
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Full document | 2vzt_full_validation.pdf.gz | 1007.2 KB | Display | |
Data in XML | 2vzt_validation.xml.gz | 66 KB | Display | |
Data in CIF | 2vzt_validation.cif.gz | 96.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/2vzt ftp://data.pdbj.org/pub/pdb/validation_reports/vz/2vzt | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 110575.758 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-1032 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Plasmid: PFD666 / Production host: STREPTOMYCES LIVIDANS (bacteria) / Strain (production host): TK24 / References: UniProt: Q56F26 #2: Chemical | ChemComp-CD / #3: Sugar | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.47 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: mother liquor containing 18% polyethylene glycol 2000 monomethylether, 20 mM CdSO4, and 100 mM Tris-HCl, pH 7.5, |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 91212 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.8 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.837 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.191 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→40 Å
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Refine LS restraints |
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