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Yorodumi- PDB-3amn: E134C-Cellobiose complex of cellulase 12A from thermotoga maritima -
+Open data
-Basic information
Entry | Database: PDB / ID: 3amn | |||||||||
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Title | E134C-Cellobiose complex of cellulase 12A from thermotoga maritima | |||||||||
Components | Endo-1,4-beta-glucanase | |||||||||
Keywords | HYDROLASE / beta jellyroll / glucanase / cellulose | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.47 Å | |||||||||
Authors | Cheng, Y.-S. / Ko, T.-P. / Liu, J.-R. / Guo, R.-T. | |||||||||
Citation | Journal: Proteins / Year: 2011 Title: Crystal structure and substrate-binding mode of cellulase 12A from Thermotoga maritima Authors: Cheng, Y.-S. / Ko, T.-P. / Wu, T.-H. / Ma, Y. / Huang, C.-H. / Lai, H.-L. / Wang, A.H.-J. / 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 | 3amn.cif.gz | 138.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3amn.ent.gz | 106.1 KB | Display | PDB format |
PDBx/mmJSON format | 3amn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3amn_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 3amn_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3amn_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 3amn_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/3amn ftp://data.pdbj.org/pub/pdb/validation_reports/am/3amn | HTTPS FTP |
-Related structure data
Related structure data | 3amhSC 3ammC 3ampC 3amqC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30753.639 Da / Num. of mol.: 2 / Mutation: E134C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: celA / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60032, cellulase #2: Polysaccharide | #3: Polysaccharide | #4: Water | ChemComp-HOH / | Nonpolymer details | SOME CELLOBIOSE MOLECULES HAVE THE ALPHA-ANOMERIC CONFIGURATION AT THE C1' IN THIS STRUCTURES. THEY ...SOME CELLOBIOSE | |
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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: 2.28 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M ammonium sulfate, 0.1M Bis-Tris, 5% glycerol, 18% PEG3350, 10mM cellobiose, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→25 Å / Num. all: 96554 / Num. obs: 94215 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 40.8 |
Reflection shell | Resolution: 1.47→1.52 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 7.8 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3AMH Resolution: 1.47→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.47→25 Å
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Refine LS restraints |
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