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- PDB-1k9e: Crystal structure of a mutated family-67 alpha-D-glucuronidase (E... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k9e | ||||||
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Title | Crystal structure of a mutated family-67 alpha-D-glucuronidase (E285N) from Bacillus stearothermophilus T-6, complexed with 4-O-methyl-glucuronic acid | ||||||
![]() | alpha-D-glucuronidase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() glucuronoxylan catabolic process / 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 | ![]() | 160.6 KB | Display | ![]() |
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PDB format | ![]() | 125.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 405.2 KB | Display | ![]() |
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Full document | ![]() | 411.1 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k9dSC ![]() 1k9fC ![]() 1l8nC ![]() 1mqpC ![]() 1mqqC ![]() 1mqrC S: Starting model for refinement 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: 78563.258 Da / Num. of mol.: 1 / Mutation: E285N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: T6 / Gene: AGUA / Plasmid: pET9d / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: Q8VVD2, UniProt: Q09LY5*PLUS, EC: 3.2.1.139 | ||
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#2: Sugar | ChemComp-GCV / | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.78 % | ||||||||||||||||||||||||||||||
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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: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 29, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9766 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40 Å / Num. obs: 72670 / % possible obs: 92.1 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.85→1.88 Å / Rmerge(I) obs: 0.234 / % possible all: 63.1 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 354446 |
Reflection shell | *PLUS % possible obs: 63.1 % |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING Starting model: PDB ENTRY 1K9D Resolution: 1.85→36.03 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 192936.65 / 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: 45.0392 Å2 / ksol: 0.374165 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→36.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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