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- PDB-4hgr: Crystal structure of E56A/K67A mutant of 2-keto-3-deoxy-D-glycero... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hgr | ||||||
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Title | Crystal structure of E56A/K67A mutant of 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase from Bacteroides thetaiotaomicron | ||||||
![]() | Acylneuraminate cytidylyltransferase | ||||||
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Function / homology | ![]() 3-deoxy-D-glycero-D-galacto-nonulopyranosonate 9-phosphatase / hydrolase activity, acting on ester bonds / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Daughtry, K.D. / Allen, K.N. | ||||||
![]() | ![]() Title: Structural Basis for the Divergence of Substrate Specificity and Biological Function within HAD Phosphatases in Lipopolysaccharide and Sialic Acid Biosynthesis. Authors: Daughtry, K.D. / Huang, H. / Malashkevich, V. / Patskovsky, Y. / Liu, W. / Ramagopal, U. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 270.8 KB | Display | ![]() |
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PDB format | ![]() | 220 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3mmzC ![]() 3mn1C ![]() 3n07C ![]() 4hgnC ![]() 4hgoC ![]() 4hgpC ![]() 4hgqC ![]() 3e8mS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18245.926 Da / Num. of mol.: 8 / Mutation: E56A, K67A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: VPI-5482 / Gene: BT_1713 / Plasmid: pET-3A-626 / Production host: ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.39 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Hepes, 150 mM magnesium chloride, 25% polyethylene glycol 3350, 3% dioxane. The crystal was dragged through paratone prior to flash-cooling, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Feb 5, 2010 / Details: Helios multi-layer optics |
Radiation | Monochromator: rotating-anode / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.05→50.73 Å / Num. all: 76062 / Num. obs: 76062 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.66 % / Rsym value: 0.1308 / Net I/σ(I): 14.12 |
Reflection shell | Resolution: 2.05→2.15 Å / Redundancy: 6.78 % / Mean I/σ(I) obs: 3.73 / Num. unique all: 9626 / Rsym value: 0.4769 / % possible all: 92.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3E8M Resolution: 2.05→50.715 Å / σ(F): 1.34 / Phase error: 26.04 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→50.715 Å
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Refine LS restraints |
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LS refinement shell |
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