[English] 日本語
Yorodumi- PDB-6mgl: Crystal structure of the catalytic domain from GH74 enzyme PoGH74... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mgl | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the catalytic domain from GH74 enzyme PoGH74 from Paenibacillus odorifer, D60A mutant in complex with XXLG and XGXXLG xyloglucan | |||||||||
Components | Xyloglucanase | |||||||||
Keywords | HYDROLASE / GLYCOSYLHYDROLASE / FAMILY GH74 / XYLOGLUCANASE / Paenibacillus odorifer / xyloglucan | |||||||||
Function / homology | Function and homology information hydrolase activity, acting on glycosyl bonds / cellulose binding / polysaccharide catabolic process Similarity search - Function | |||||||||
Biological species | Paenibacillus odorifer (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Stogios, P.J. / Skarina, T. / Arnal, G. / Watanabe, N. / Brumer, H. / Savchenko, A. | |||||||||
Funding support | Canada, 1items
| |||||||||
Citation | Journal: Biochem. J. / Year: 2018 Title: Structural enzymology reveals the molecular basis of substrate regiospecificity and processivity of an exemplar bacterial glycoside hydrolase family 74endo-xyloglucanase. Authors: Arnal, G. / Stogios, P.J. / Asohan, J. / Skarina, T. / Savchenko, A. / Brumer, H. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6mgl.cif.gz | 340.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6mgl.ent.gz | 270.7 KB | Display | PDB format |
PDBx/mmJSON format | 6mgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/6mgl ftp://data.pdbj.org/pub/pdb/validation_reports/mg/6mgl | HTTPS FTP |
---|
-Related structure data
Related structure data | 6mgjC 6mgkC 2cn3S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 80139.258 Da / Num. of mol.: 1 / Mutation: D60A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus odorifer (bacteria) / Gene: BSK60_29080 / Plasmid: p15TV-Lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1R0YRH0 |
---|
-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#3: Polysaccharide | alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-[alpha-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 1408 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PE3 / | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | The sequence of xyloglucanase is from GenBank: AIQ73809 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.08 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 0.2 M magnesium chloride, 25% PEG33530, xyloglucan mixture |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→46.41 Å / Num. obs: 117368 / % possible obs: 99.5 % / Redundancy: 4 % / CC1/2: 0.701 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.031 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / Num. unique obs: 5486 / CC1/2: 0.701 / Rpim(I) all: 0.352 / % possible all: 94.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CN3 Resolution: 1.5→46.41 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.21
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→46.41 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|