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- PDB-1k9f: 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: 1k9f | |||||||||
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Title | Crystal structure of a mutated family-67 alpha-D-glucuronidase (E285N) from Bacillus stearothermophilus T-6, complexed with aldotetraouronic acid | |||||||||
![]() | alpha-D-glucuronidase | |||||||||
![]() | HYDROLASE | |||||||||
Function / homology | ![]() glucuronoxylan catabolic process / xylan alpha-1,2-glucuronosidase / xylan alpha-1,2-glucuronosidase activity / alpha-glucuronidase activity / 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 | ![]() | 161.6 KB | Display | ![]() |
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PDB format | ![]() | 126 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.5 KB | Display | ![]() |
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Full document | ![]() | 483.1 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k9dSC ![]() 1k9eC ![]() 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: plasmid / Species (production host): Escherichia coli / Production host: ![]() ![]() References: GenBank: 16876433, UniProt: Q09LY5*PLUS, EC: 3.2.1.139 | ||
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#2: Polysaccharide | 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-GOL / #4: 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 293.0K | ||||||||||||||||||||||||||||||
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: Oct 5, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.039 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. obs: 85011 / % possible obs: 91.6 % / Redundancy: 7 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.75→1.78 Å / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 5 / % possible all: 58.4 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 664504 |
Reflection shell | *PLUS % possible obs: 58.4 % |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING Starting model: PDB ENTRY 1K9D Resolution: 1.75→36.55 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 139358.23 / 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: 52.0365 Å2 / ksol: 0.377919 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→36.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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