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Yorodumi- PDB-1ksc: The structure of Endoglucanase from termite, Nasutitermes takasag... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ksc | ||||||
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Title | The structure of Endoglucanase from termite, Nasutitermes takasagoensis, at pH 5.6. | ||||||
Components | Endo-b-1,4-glucanase | ||||||
Keywords | HYDROLASE / Cellulase / Endoglucanase / Termite / Nasutitermes takasagoensis / Glycosyl Hydrolase / Family 9 / (Alpha/Alpha)6 | ||||||
Function / homology | Function and homology information cellulase / cellulase activity / cellulose catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Nasutitermes takasagoensis (cockroach) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Khademi, S. / Guarino, L.A. / Watanabe, H. / Tokuda, G. / Meyer, E.F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structure of an endoglucanase from termite, Nasutitermes takasagoensis. Authors: Khademi, S. / Guarino, L.A. / Watanabe, H. / Tokuda, G. / Meyer, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ksc.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ksc.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ksc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/1ksc ftp://data.pdbj.org/pub/pdb/validation_reports/ks/1ksc | HTTPS FTP |
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-Related structure data
Related structure data | 1ks8C 1ksdC 3tf4S 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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Unit cell |
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-Components
#1: Protein | Mass: 47844.309 Da / Num. of mol.: 1 / Fragment: Catalytic Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nasutitermes takasagoensis (cockroach) / Plasmid: pET3a-Nts / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O77044, cellulase |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.01 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Ammonium Sulfate, Sodium Citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 5.6 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.5 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MAC Science DIP-2030K / Detector: IMAGE PLATE / Date: Jun 1, 2000 / Details: mirrors |
Radiation | Monochromator: OSMIC, Model 140-000023 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30 Å / Num. all: 61593 / Num. obs: 70043 / % possible obs: 93.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 18.73 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.45→1.5 Å / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 3.6 / % possible all: 83.8 |
Reflection | *PLUS Highest resolution: 1.55 Å / Lowest resolution: 30 Å / Num. obs: 60004 / Num. measured all: 1124141 |
Reflection shell | *PLUS Highest resolution: 1.55 Å / Lowest resolution: 1.61 Å / % possible obs: 83.8 % / Rmerge(I) obs: 0.562 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TF4 Resolution: 1.55→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: 0.373825 / ksol: 56.4412 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.61 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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