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Yorodumi- PDB-6ufl: Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ufl | |||||||||
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Title | Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei (AmGH128_I) in the complex with laminarihexaose | |||||||||
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 / Asl1-like glycosyl hydrolase catalytic domain-containing protein Function and homology information | |||||||||
Biological species | Amycolatopsis mediterranei (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | |||||||||
Authors | Cordeiro, R.L. / Domingues, M.N. / Vieira, P.S. / 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 | 6ufl.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ufl.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ufl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ufl_validation.pdf.gz | 717.4 KB | Display | wwPDB validaton report |
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Full document | 6ufl_full_validation.pdf.gz | 720 KB | Display | |
Data in XML | 6ufl_validation.xml.gz | 14 KB | Display | |
Data in CIF | 6ufl_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/6ufl ftp://data.pdbj.org/pub/pdb/validation_reports/uf/6ufl | HTTPS FTP |
-Related structure data
Related structure data | 6uaqC 6uarC 6uasC 6uatC 6uauC 6uavC 6uawC 6uaxC 6uayC 6uazC 6ub0C 6ub1C 6ub2C 6ub3C 6ub4C 6ub5C 6ub6C 6ub7C 6ub8C 6ubaC 6ubbC 6ubcC 6ubdC 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
#1: Protein | Mass: 27916.943 Da / Num. of mol.: 1 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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#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: 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: 2.41 Å3/Da / Density % sol: 49.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 20% (w/v) Polyethylene glycol 3.350, 0.2 M Potassium Thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→50 Å / Num. obs: 32212 / % possible obs: 94 % / Redundancy: 3 % / CC1/2: 0.995 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.61→1.71 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4967 / CC1/2: 0.835 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→45.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.101 Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
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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 mean: 20.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→45.47 Å
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Refine LS restraints |
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