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- PDB-1k9d: The 1.7 A crystal structure of alpha-D-glucuronidase, a family-67... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k9d | ||||||
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Title | The 1.7 A crystal structure of alpha-D-glucuronidase, a family-67 glycoside hydrolase from Bacillus stearothermophilus T-1 | ||||||
![]() | alpha-D-glucuronidase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() xylan alpha-1,2-glucuronosidase / xylan alpha-1,2-glucuronosidase activity / alpha-glucuronidase activity / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Golan, G. / Shallom, D. / Teplitsky, A. / Zaide, G. / Shulami, S. / Baasov, T. / Stojanoff, V. / Thompson, A. / Shoham, Y. / Shoham, G. | ||||||
![]() | ![]() Title: Crystal Structures of Geobacillus stearothermophilus {alpha}-Glucuronidase Complexed with Its Substrate and Products: MECHANISTIC IMPLICATIONS. Authors: Golan, G. / Shallom, D. / Teplitsky, A. / Zaide, G. / Shulami, S. / Baasov, T. / Stojanoff, V. / Thompson, A. / Shoham, Y. / Shoham, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.8 KB | Display | ![]() |
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PDB format | ![]() | 131.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383.1 KB | Display | ![]() |
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Full document | ![]() | 389.3 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k9eC ![]() 1k9fC ![]() 1l8nC ![]() 1mqpC ![]() 1mqqC ![]() 1mqrC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 78579.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: T1 / Gene: AGUA / Plasmid: pET9d / Species (production host): Escherichia coli / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.69 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M Na-citrate pH 5.0, 14% PEG 4000, 12% Iso-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / PH range low: 5.5 / PH range high: 5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 94808 / Redundancy: 4 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.382 / Num. unique all: 3008 / % possible all: 60.7 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 50 Å / % possible obs: 93.5 % / Num. measured all: 271828 |
Reflection shell | *PLUS % possible obs: 60.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: initial and partial model based on 2.4A resolution data (unpublished) Resolution: 1.7→35.9 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 274221.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.864 Å2 / ksol: 0.366973 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→35.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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