+Open data
-Basic information
Entry | Database: PDB / ID: 2zuy | ||||||
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Title | Crystal structure of exotype rhamnogalacturonan lyase YesX | ||||||
Components | YesX protein | ||||||
Keywords | LYASE / Beta-propeller | ||||||
Function / homology | Function and homology information rhamnogalacturonan exolyase / cell wall organization / lyase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Ochiai, A. / Itoh, T. / Mikami, B. / Hashimoto, W. / Murata, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases Authors: Ochiai, A. / Itoh, T. / Mikami, B. / Hashimoto, W. / Murata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zuy.cif.gz | 155 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zuy.ent.gz | 118.3 KB | Display | PDB format |
PDBx/mmJSON format | 2zuy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zuy_validation.pdf.gz | 428.8 KB | Display | wwPDB validaton report |
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Full document | 2zuy_full_validation.pdf.gz | 432 KB | Display | |
Data in XML | 2zuy_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 2zuy_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/2zuy ftp://data.pdbj.org/pub/pdb/validation_reports/zu/2zuy | HTTPS FTP |
-Related structure data
Related structure data | 2zuxC 2z8rS 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
#1: Protein | Mass: 68846.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yesX, BSU07060 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)pLysS References: UniProt: O31527, Lyases; Carbon-oxygen lyases; Acting on polysaccharides | ||
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#2: Chemical | ChemComp-CA / #3: 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: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 20% PEG 3350, 0.2M Ammonium acetate, pH7.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 20, 2008 / Details: mirror |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 77151 / % possible obs: 98.9 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 4.1 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z8R Resolution: 1.65→37.19 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.439 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.087 / 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: 10.801 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→37.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.652→1.695 Å / Total num. of bins used: 20
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