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Yorodumi- PDB-2zux: Crystal structure of rhamnogalacturonan lyase YesW complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zux | ||||||
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Title | Crystal structure of rhamnogalacturonan lyase YesW complexed with rhamnose | ||||||
Components | YesW protein | ||||||
Keywords | LYASE / Beta-propeller / Rhamnose complex | ||||||
Function / homology | Function and homology information rhamnogalacturonan endolyase / rhamnogalacturonan endolyase activity / cell wall organization / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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 | 2zux.cif.gz | 268.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zux.ent.gz | 211.7 KB | Display | PDB format |
PDBx/mmJSON format | 2zux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zux_validation.pdf.gz | 473.5 KB | Display | wwPDB validaton report |
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Full document | 2zux_full_validation.pdf.gz | 484.6 KB | Display | |
Data in XML | 2zux_validation.xml.gz | 54.4 KB | Display | |
Data in CIF | 2zux_validation.cif.gz | 83.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/2zux ftp://data.pdbj.org/pub/pdb/validation_reports/zu/2zux | HTTPS FTP |
-Related structure data
Related structure data | 2zuyC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 64520.133 Da / Num. of mol.: 2 / Fragment: UNP residues 38-620 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yesW, BSU07050 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) References: UniProt: O31526, Lyases; Carbon-oxygen lyases; Acting on polysaccharides #2: Chemical | ChemComp-CA / #3: Sugar | ChemComp-RAM / #4: Chemical | #5: 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: 2.36 Å3/Da / Density % sol: 47.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: 55% MPD, 0.1M TRIS, pH8.4, 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: 0.8 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: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→50 Å / Num. obs: 280440 / % possible obs: 97.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.32→1.37 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.8 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z8R Resolution: 1.32→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.667 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.049 / 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: 16.536 Å2
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Refinement step | Cycle: LAST / Resolution: 1.32→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.319→1.353 Å / Total num. of bins used: 20
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