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Yorodumi- PDB-3axx: Functional analysis of hyperthermophilic endocellulase from the A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3axx | |||||||||
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Title | Functional analysis of hyperthermophilic endocellulase from the Archaeon Pyrococcus horikoshii | |||||||||
Components | 458aa long hypothetical endo-1,4-beta-glucanase | |||||||||
Keywords | HYDROLASE / TIM barrel | |||||||||
Function / homology | Function and homology information polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | |||||||||
Biological species | Pyrococcus horikoshii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Kim, H.-W. / Ishikawa, K. | |||||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: Functional analysis of hyperthermophilic endocellulase from Pyrococcus horikoshii by crystallographic snapshots Authors: Kim, H.-W. / Ishikawa, K. #1: Journal: Proteins / Year: 2010 Title: Structure of hyperthermophilic endocellulase from Pyrococcus horikoshii Authors: Kim, H.W. / Ishikawa, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3axx.cif.gz | 249 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3axx.ent.gz | 200 KB | Display | PDB format |
PDBx/mmJSON format | 3axx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3axx_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 3axx_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 3axx_validation.xml.gz | 49.1 KB | Display | |
Data in CIF | 3axx_validation.cif.gz | 69.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/3axx ftp://data.pdbj.org/pub/pdb/validation_reports/ax/3axx | HTTPS FTP |
-Related structure data
Related structure data | 3qhmC 3qhnC 3qhoC 2zumS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 51982.879 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: EGPh, PH1171 / Plasmid: pET11a / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): BL21(DE3) / References: UniProt: O58925, cellulase #2: Polysaccharide | #3: Chemical | #4: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 1.99 Å3/Da / Density % sol: 38.22 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.5M ammonium phosphate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Detector: IMAGE PLATE / Date: Mar 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 97064 / Num. obs: 94740 / % possible obs: 97.6 % / Redundancy: 3.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZUM Resolution: 1.9→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
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Solvent computation | Bsol: 74.2861 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.52 Å2 / Biso mean: 36.6026 Å2 / Biso min: 9.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å /
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Xplor file |
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