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- PDB-4gvg: Crystal structure of Salmonella typhimurium family 3 glycoside hy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4gvg | ||||||
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Title | Crystal structure of Salmonella typhimurium family 3 glycoside hydrolase (NagZ) | ||||||
![]() | Beta-hexosaminidase | ||||||
![]() | HYDROLASE / TIM-BARREL | ||||||
Function / homology | ![]() beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division ...beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division / response to antibiotic / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bacik, J.P. / Mark, B.L. | ||||||
![]() | ![]() Title: Active Site Plasticity within the Glycoside Hydrolase NagZ Underlies a Dynamic Mechanism of Substrate Distortion. Authors: Bacik, J.P. / Whitworth, G.E. / Stubbs, K.A. / Vocadlo, D.J. / Mark, B.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153 KB | Display | ![]() |
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PDB format | ![]() | 119.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452 KB | Display | ![]() |
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Full document | ![]() | 456.3 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 49 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gvfC ![]() 4gvhC ![]() 4gviC ![]() 4gyjC ![]() 4gykC ![]() 1tr9S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38723.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: nagZ, STM1209 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.32 % |
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Crystal grow | Temperature: 296 K / pH: 6.5 Details: 0.1 M MES, 25% PEG 1000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→38.32 Å / Num. obs: 67010 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 14.27 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.123 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.524 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TR9 Resolution: 1.7→38.32 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 19.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.88 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→38.32 Å
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Refine LS restraints |
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LS refinement shell |
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