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- PDB-1ksd: The structure of Endoglucanase from termite, Nasutitermes takasag... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ksd | ||||||
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Title | The structure of Endoglucanase from termite, Nasutitermes takasagoensis, at pH 6.5. | ||||||
![]() | Endo-b-1,4-glucanase | ||||||
![]() | HYDROLASE / Cellulase / Endoglucanase / Termite / Nasutitermes takasagoensis / Glycosyl Hydrolase / Family 9 / (Alpha/Alpha)6 | ||||||
Function / homology | ![]() cellulase / cellulase activity / cellulose catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Khademi, S. / Guarino, L.A. / Watanabe, H. / Tokuda, G. / Meyer, E.F. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.4 KB | Display | ![]() |
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PDB format | ![]() | 85.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 412.3 KB | Display | ![]() |
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Full document | ![]() | 416.2 KB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 38.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ks8C ![]() 1kscC ![]() 3tf4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.12 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ammonium Sulfate, Sodium Citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.5 | ||||||||||||||||||||||||
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: ![]() |
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: 1.6→30 Å / Num. all: 58967 / Num. obs: 57195 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 19.7 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 3.6 / % possible all: 92.4 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 654717 |
Reflection shell | *PLUS % possible obs: 92.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3TF4 Resolution: 1.6→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.2325 Å2 / ksol: 0.378856 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.011 / 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 / Rfactor Rfree: 0.201 / Rfactor Rwork: 0.178 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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