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Yorodumi- PDB-4ha4: Structure of beta-glycosidase from Acidilobus saccharovorans in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ha4 | ||||||
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Title | Structure of beta-glycosidase from Acidilobus saccharovorans in complex with glycerol | ||||||
Components | Beta-galactosidase | ||||||
Keywords | HYDROLASE / TIM barrel / beta-glycosidase | ||||||
Function / homology | Function and homology information beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Acidilobus saccharovorans (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | ||||||
Authors | Trofimov, A.A. / Polyakov, K.M. / Tikhonov, A.V. / Bezsudnova, E.Y. / Dorovatovskii, P.V. / Gumerov, V.M. / Ravin, N.V. / Skryabin, K.G. / Popov, V.O. | ||||||
Citation | Journal: Dokl.Biochem.Biophys. Title: Structures of beta-glycosidase from Acidilobus saccharovorans in complexes with tris and glycerol. Authors: Trofimov, A.A. / Polyakov, K.M. / Tikhonov, A.V. / Bezsudnova, E.Y. / Dorovatovskii, P.V. / Gumerov, V.M. / Ravin, N.V. / Skryabin, K.G. / Popov, V.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ha4.cif.gz | 228 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ha4.ent.gz | 189.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ha4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/4ha4 ftp://data.pdbj.org/pub/pdb/validation_reports/ha/4ha4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55456.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidilobus saccharovorans (archaea) / Strain: DSM 16705 / VKM B-2471 / 345-15 / Gene: ASAC1390, ASAC_1390 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): DLT1270 (pRARE2) / References: UniProt: D9PZ08, beta-galactosidase |
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-Non-polymers , 6 types, 556 molecules
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | ChemComp-SIN / | ||||||
#4: Chemical | #5: Chemical | ChemComp-PG4 / #6: Chemical | ChemComp-PG6 / | #7: 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: 2.65 Å3/Da / Density % sol: 53.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Protein solution (1.5mcl): 13mg/ml Asbeta-Gly, 0.025M NaCl, 0.025M Hepes (pH 7.5). Reservoir solution (1.5mcl): 1.0M succinic acid (pH 7.0), 0.1M Hepes (pH 7.0), 1% w/v polyethylene glycol ...Details: Protein solution (1.5mcl): 13mg/ml Asbeta-Gly, 0.025M NaCl, 0.025M Hepes (pH 7.5). Reservoir solution (1.5mcl): 1.0M succinic acid (pH 7.0), 0.1M Hepes (pH 7.0), 1% w/v polyethylene glycol monomethyl ether 2000. The crystal was soaked in a cryoprotection solution containing 20% v/v glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.9815 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9815 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→19.827 Å / Num. obs: 124046 / % possible obs: 98.8 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.37→1.45 Å / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.1 / Num. unique all: 18722 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→19.827 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.533 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.045 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.182 Å2
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Refine analyze | Luzzati coordinate error obs: 0.134 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→19.827 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.37→1.406 Å / Total num. of bins used: 20
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