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Yorodumi- PDB-3azr: Diverse Substrates Recognition Mechanism Revealed by Thermotoga m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3azr | |||||||||
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Title | Diverse Substrates Recognition Mechanism Revealed by Thermotoga maritima Cel5A Structures in Complex with Cellobiose | |||||||||
Components | Endoglucanase | |||||||||
Keywords | HYDROLASE / cellulose / cellulase / biofuel / Tim Barrel | |||||||||
Function / homology | Function and homology information glucan catabolic process / beta-glucosidase activity / cell surface / extracellular region Similarity search - Function | |||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | |||||||||
Authors | Wu, T.H. / Huang, C.H. / Ko, T.P. / Lai, H.L. / Ma, Y. / Chen, C.C. / Cheng, Y.S. / Liu, J.R. / Guo, R.T. | |||||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2011 Title: Diverse substrate recognition mechanism revealed by Thermotoga maritima Cel5A structures in complex with cellotetraose, cellobiose and mannotriose Authors: Wu, T.H. / Huang, C.H. / Ko, T.P. / Lai, H.L. / Ma, Y. / Chen, C.C. / Cheng, Y.S. / Liu, J.R. / Guo, R.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3azr.cif.gz | 152.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3azr.ent.gz | 119.7 KB | Display | PDB format |
PDBx/mmJSON format | 3azr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3azr_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3azr_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3azr_validation.xml.gz | 31 KB | Display | |
Data in CIF | 3azr_validation.cif.gz | 46.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/3azr ftp://data.pdbj.org/pub/pdb/validation_reports/az/3azr | HTTPS FTP |
-Related structure data
Related structure data | 3amcC 3amdC 3amgC 3aofC 3azsC 3aztC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37380.488 Da / Num. of mol.: 2 / Mutation: E253A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM_1751 / Plasmid: pET32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9X273, cellulase #2: Polysaccharide | #3: Sugar | #4: 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 Å3/Da / Density % sol: 38.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M tris pH8.5 , 0.4M NaCl, 28% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→25 Å / Num. obs: 62921 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rsym value: 0.035 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.71→1.77 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 6264 / Rsym value: 0.479 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→24.98 Å / σ(F): 2 / Stereochemistry target values: ML
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Solvent computation | Bsol: 54.775 Å2 | |||||||||||||||||||||
Displacement parameters | Biso mean: 22.6196 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→24.98 Å
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Refine LS restraints |
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Xplor file |
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