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Yorodumi- PDB-2z8s: Crystal structure of rhamnogalacturonan lyase YesW complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z8s | |||||||||
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Title | Crystal structure of rhamnogalacturonan lyase YesW complexed with digalacturonic acid | |||||||||
Components | YesW proteinRhamnogalacturonan endolyase | |||||||||
Keywords | LYASE / BETA-PROPELLER | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Ochiai, A. / Itoh, T. / Maruyama, Y. / Kawamata, A. / Mikami, B. / Hashimoto, W. / Murata, K. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER Authors: Ochiai, A. / Itoh, T. / Maruyama, Y. / Kawamata, A. / 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 | 2z8s.cif.gz | 242 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z8s.ent.gz | 191.1 KB | Display | PDB format |
PDBx/mmJSON format | 2z8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/2z8s ftp://data.pdbj.org/pub/pdb/validation_reports/z8/2z8s | HTTPS FTP |
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-Related structure data
Related structure data | 2z8rSC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4 / Auth seq-ID: 38 - 537 / Label seq-ID: 1 - 500
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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 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) References: UniProt: O31526, Lyases; Carbon-oxygen lyases; Acting on polysaccharides #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CA / #4: 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: 2.31 Å3/Da / Density % sol: 46.81 % |
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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 293.0K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 21, 2007 |
Radiation | Monochromator: Carbon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→26.2 Å / Num. obs: 37253 / % possible obs: 93.3 % / Redundancy: 1.53 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.059 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 1.14 % / Mean I/σ(I) obs: 2.41 / Rsym value: 0.233 / % possible all: 70 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z8R Resolution: 2.5→26.15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.876 / SU B: 10.998 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 21.003 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→26.15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3504 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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