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Yorodumi- PDB-6uaw: Crystal structure of a GH128 (subgroup II) endo-beta-1,3-glucanas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uaw | |||||||||
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Title | Crystal structure of a GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava (PvGH128_II) in complex with laminaritriose | |||||||||
Components | Glyco_hydro_cc domain-containing protein | |||||||||
Keywords | HYDROLASE / Glycosyl hydrolase / CARBOHYDRATE | |||||||||
Function / homology | : / fungal-type cell wall polysaccharide metabolic process / Uncharacterised protein family, glycosyl hydrolase catalytic domain / Glycosyl hydrolase catalytic core / fungal-type cell wall / Glycoside hydrolase superfamily / Asl1-like glycosyl hydrolase catalytic domain-containing protein Function and homology information | |||||||||
Biological species | Pseudomonas viridiflava (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Santos, C.R. / Costa, P.A.C.R. / Lima, E.A. / Mandelli, F. / 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 | 6uaw.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uaw.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 6uaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uaw_validation.pdf.gz | 753.4 KB | Display | wwPDB validaton report |
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Full document | 6uaw_full_validation.pdf.gz | 753.7 KB | Display | |
Data in XML | 6uaw_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 6uaw_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/6uaw ftp://data.pdbj.org/pub/pdb/validation_reports/ua/6uaw | HTTPS FTP |
-Related structure data
Related structure data | 6uaqC 6uarC 6uasC 6uatC 6uauC 6uavSC 6uaxC 6uayC 6uazC 6ub0C 6ub1C 6ub2C 6ub3C 6ub4C 6ub5C 6ub6C 6ub7C 6ub8C 6ubaC 6ubbC 6ubcC 6ubdC 6uflC 6ufzC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32102.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas viridiflava (bacteria) / Gene: CFBP1590__2373 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y6JJH6 | ||||
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#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: bis-tris 0.1 M ammonium sulfate 2 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: 1.23986 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23986 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→27.18 Å / Num. obs: 36122 / % possible obs: 97.6 % / Redundancy: 6.39 % / CC1/2: 0.999 / Net I/σ(I): 15.36 |
Reflection shell | Resolution: 1.5→1.59 Å / Mean I/σ(I) obs: 2.53 / Num. unique obs: 5890 / CC1/2: 0.838 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6UAV Resolution: 1.5→27.18 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.164 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.079 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 61.14 Å2 / Biso mean: 18.233 Å2 / Biso min: 9.57 Å2
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Refinement step | Cycle: final / Resolution: 1.5→27.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 34.3102 Å / Origin y: 14.3576 Å / Origin z: 19.9688 Å
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