+Open data
-Basic information
Entry | Database: PDB / ID: 5t4g | |||||||||
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Title | Crystal structure of BhGH81 in complex with laminarin | |||||||||
Components | Glycoside Hydrolase | |||||||||
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 / cell surface / extracellular region Similarity search - Function | |||||||||
Biological species | Bacillus halodurans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | |||||||||
Authors | Pluvinage, B. / Boraston, A.B. | |||||||||
Funding support | Canada, 1items
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Citation | Journal: Structure / Year: 2017 Title: Structural Analysis of a Family 81 Glycoside Hydrolase Implicates Its Recognition of beta-1,3-Glucan Quaternary Structure. 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 | 5t4g.cif.gz | 190.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t4g.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 5t4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t4g_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5t4g_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5t4g_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 5t4g_validation.cif.gz | 54.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/5t4g ftp://data.pdbj.org/pub/pdb/validation_reports/t4/5t4g | HTTPS FTP |
-Related structure data
Related structure data | 5t49SC 5t4aC 5t4cC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 88442.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (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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-Sugars , 3 types, 3 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose |
#4: 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-(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 |
-Non-polymers , 3 types, 686 molecules
#5: Chemical | ChemComp-PO4 / #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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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: 2.92 Å3/Da / Density % sol: 57.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 1.4 M NaH2PO4, 0.2 M K2HPO4, 0.1 M citric acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 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: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→82.55 Å / Num. obs: 85487 / % possible obs: 92.2 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 4.4 / CC1/2: 0.887 / % possible all: 88.3 |
-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: 1.8→82.55 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.08 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.099 / 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: 78.31 Å2 / Biso mean: 18.254 Å2 / Biso min: 4.61 Å2
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Refinement step | Cycle: final / Resolution: 1.8→82.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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