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Yorodumi- PDB-2eo7: Crystal structure of Cel44A, GH family 44 endoglucanase from Clos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eo7 | |||||||||
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Title | Crystal structure of Cel44A, GH family 44 endoglucanase from Clostridium thermocellum | |||||||||
Components | Endoglucanase | |||||||||
Keywords | HYDROLASE / TIM-barrel / TIM-like barrel / beta-sandwich / The composite domain of GH family 5 / 30 / 39 / 51 | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Clostridium thermocellum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Kitao, Y. / Karita, S. / Watanabe, N. / Sakka, K. / Tanaka, I. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal structure of Cel44A, a glycoside hydrolase family 44 endoglucanase from Clostridium thermocellum. Authors: Kitago, Y. / Karita, S. / Watanabe, N. / Kamiya, M. / Aizawa, T. / Sakka, K. / Tanaka, I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eo7.cif.gz | 129.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eo7.ent.gz | 97.2 KB | Display | PDB format |
PDBx/mmJSON format | 2eo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2eo7_validation.pdf.gz | 725 KB | Display | wwPDB validaton report |
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Full document | 2eo7_full_validation.pdf.gz | 728.6 KB | Display | |
Data in XML | 2eo7_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 2eo7_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/2eo7 ftp://data.pdbj.org/pub/pdb/validation_reports/eo/2eo7 | HTTPS FTP |
-Related structure data
Related structure data | 2e0pC 2e4tSC 2eexC 2ej1C 2eqdC 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 / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 57688.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: F1 / Gene: CelJ, CelJ-Cel44A / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P71140, cellulase, xyloglucan-specific endo-beta-1,4-glucanase |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotetraose |
-Non-polymers , 5 types, 460 molecules
#3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-CL / | #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: 2.09 Å3/Da / Density % sol: 41.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES-NaOH pH6.5, 6mM ZnSO4, 16%(w/v) PEG MME 550, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2006 / Details: mirrors |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 49922 / Num. obs: 49772 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 13.9 Å2 / Rsym value: 0.068 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 4811 / Rsym value: 0.216 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E4T Resolution: 1.75→19.69 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1940898.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.3913 Å2 / ksol: 0.387212 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→19.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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