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Yorodumi- PDB-2okx: Crystal structure of GH78 family rhamnosidase of Bacillus SP. GL1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2okx | ||||||
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Title | Crystal structure of GH78 family rhamnosidase of Bacillus SP. GL1 AT 1.9 A | ||||||
Components | Rhamnosidase B | ||||||
Keywords | HYDROLASE / alpha barrel / rhamnosidase / glycoside hydrolase family 78 / invertase | ||||||
Function / homology | Function and homology information alpha-L-rhamnosidase / alpha-L-rhamnosidase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.9 Å | ||||||
Authors | Cui, Z. / Mikami, B. / Hashimoto, W. / Murata, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal Structure of Glycoside Hydrolase Family 78 alpha-L-Rhamnosidase from Bacillus sp. GL1 Authors: Cui, Z. / Maruyama, Y. / 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 | 2okx.cif.gz | 428.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2okx.ent.gz | 343.3 KB | Display | PDB format |
PDBx/mmJSON format | 2okx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/2okx ftp://data.pdbj.org/pub/pdb/validation_reports/ok/2okx | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 106153.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: GL1 / Gene: rhaB / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93RE7, alpha-L-rhamnosidase #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 13.5%(W/V) PEG 8000, 0.08M sodium cacodylate, 0.16M calcium acetate, 20%(V/V) glycerol, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.9→49.4 Å / Num. obs: 188971 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.2 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.1 / % possible all: 91 |
-Phasing
Phasing | Method: MAD | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm | FOM : 0.78 / FOM acentric: 0.79 / FOM centric: 0.74 / Reflection: 80307 / Reflection acentric: 73605 / Reflection centric: 6702 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: SAD MODEL Resolution: 1.9→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3179334.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.06 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
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Xplor file |
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