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Yorodumi- PDB-6uau: Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uau | |||||||||
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Title | Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei (AmGH128_I) in complex with laminaritriose and laminaribiose | |||||||||
Components | Glyco_hydro_cc domain-containing protein | |||||||||
Keywords | HYDROLASE / Glycosyl hydrolase / CARBOHYDRATE | |||||||||
Function / homology | Uncharacterised protein family, glycosyl hydrolase catalytic domain / Glycosyl hydrolase catalytic core / Glycoside hydrolase superfamily / beta-laminaribiose / DI(HYDROXYETHYL)ETHER / Asl1-like glycosyl hydrolase catalytic domain-containing protein Function and homology information | |||||||||
Biological species | Amycolatopsis mediterranei (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Vieira, P.S. / Cabral, L. / Costa, P.A.C.R. / Santos, C.R. / Murakami, M.T. | |||||||||
Funding support | Brazil, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2020 Title: Structural insights into beta-1,3-glucan cleavage by a glycoside hydrolase family. Authors: Santos, C.R. / Costa, P.A.C.R. / Vieira, P.S. / Gonzalez, S.E.T. / Correa, T.L.R. / Lima, E.A. / Mandelli, F. / Pirolla, R.A.S. / Domingues, M.N. / Cabral, L. / Martins, M.P. / Cordeiro, R.L. ...Authors: Santos, C.R. / Costa, P.A.C.R. / Vieira, P.S. / Gonzalez, S.E.T. / Correa, T.L.R. / Lima, E.A. / Mandelli, F. / Pirolla, R.A.S. / Domingues, M.N. / Cabral, L. / Martins, M.P. / Cordeiro, R.L. / Junior, A.T. / Souza, B.P. / Prates, E.T. / Gozzo, F.C. / Persinoti, G.F. / Skaf, M.S. / Murakami, M.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uau.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uau.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 6uau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/6uau ftp://data.pdbj.org/pub/pdb/validation_reports/ua/6uau | HTTPS FTP |
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-Related structure data
Related structure data | 6uaqC 6uarC 6uasC 6uatC 6uavC 6uawC 6uaxC 6uayC 6uazC 6ub0C 6ub1C 6ub2C 6ub3C 6ub4C 6ub5C 6ub6C 6ub7C 6ub8C 6ubaC 6ubbC 6ubcC 6ubdC 6uflC 6ufzC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27859.891 Da / Num. of mol.: 1 / Mutation: E102A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis mediterranei (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: G0FQ07 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose |
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#3: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 260 molecules
#4: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-PEG / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.77 Å3/Da / Density % sol: 55.61 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Zinc Chloride 0.01 M PEG 6000 15% Sodium acetate 0.1 M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.458 Å / Relative weight: 1 |
Reflection | Resolution: 1.897→45.98 Å / Num. obs: 21936 / % possible obs: 99 % / Redundancy: 3.82 % / CC1/2: 0.995 / Net I/σ(I): 9.54 |
Reflection shell | Resolution: 1.897→2.01 Å / Num. unique obs: 3478 / CC1/2: 0.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.97 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.144 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.53 Å2 / Biso mean: 20.563 Å2 / Biso min: 12.7 Å2
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Refinement step | Cycle: final / Resolution: 1.9→45.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.946 Å
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