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Yorodumi- PDB-5upi: Crystal structure of BhGH81 mutant in complex with laminaro-biose -
+Open data
-Basic information
Entry | Database: PDB / ID: 5upi | |||||||||
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Title | Crystal structure of BhGH81 mutant in complex with laminaro-biose | |||||||||
Components | BH0236 protein | |||||||||
Keywords | HYDROLASE / (alpha/beta)6 barrel / glycoside hydrolase | |||||||||
Function / homology | Function and homology information : / endo-1,3(4)-beta-glucanase activity / glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / polysaccharide catabolic process / cell wall organization / carbohydrate binding / extracellular region Similarity search - Function | |||||||||
Biological species | Bacillus halodurans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | |||||||||
Authors | Pluvinage, B. / Boraston, A.B. | |||||||||
Citation | Journal: Structure / Year: 2017 Title: The quaternary structure of beta-1,3-glucan contributes to its recognition and hydrolysis by a multimodular family 81 glycoside hydrolase Authors: Pluvinage, B. / Fillo, A. / Massel, P. / Boraston, A.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5upi.cif.gz | 190.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5upi.ent.gz | 146.2 KB | Display | PDB format |
PDBx/mmJSON format | 5upi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5upi_validation.pdf.gz | 1014 KB | Display | wwPDB validaton report |
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Full document | 5upi_full_validation.pdf.gz | 1015.5 KB | Display | |
Data in XML | 5upi_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 5upi_validation.cif.gz | 56.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/5upi ftp://data.pdbj.org/pub/pdb/validation_reports/up/5upi | HTTPS FTP |
-Related structure data
Related structure data | 5upmC 5upnC 5upoC 5v1wC 5t49S C: citing same article (ref.) S: Starting model for refinement |
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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: 85277.633 Da / Num. of mol.: 1 / Fragment: residues 28-779 / Mutation: E542Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (bacteria) Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125 Gene: BH0236 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KG76 | ||||||
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#2: Polysaccharide | #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-EDO / #5: 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: 2.88 Å3/Da / Density % sol: 57.24 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 15% PEG 10000, 0.2 M ammonium acetate, 0.1 M bis-tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97971 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97971 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→80.78 Å / Num. obs: 117552 / % possible obs: 99 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.031 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 4.6 / CC1/2: 0.934 / Rpim(I) all: 0.136 / % possible all: 93.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T49 Resolution: 1.65→80.78 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.249 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.071 / Details: 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: 56.82 Å2 / Biso mean: 14.176 Å2 / Biso min: 1.42 Å2
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Refinement step | Cycle: final / Resolution: 1.65→80.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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