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- PDB-4hgn: Crystal Structure of 2-keto-3-deoxyoctulosonate 8-phosphate PHOSP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hgn | ||||||
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Title | Crystal Structure of 2-keto-3-deoxyoctulosonate 8-phosphate PHOSPHOHYDROLASE from Bacteroides thetaiotaomicron | ||||||
![]() | 2-keto-3-deoxy-D-manno-octulosonate 8-phosphate phosphohydrolase | ||||||
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Function / homology | ![]() | ||||||
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 | ![]() | 144.4 KB | Display | ![]() |
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PDB format | ![]() | 112.1 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 ![]() 4hgoC ![]() 4hgpC ![]() 4hgqC ![]() 4hgrC ![]() 3e8mS 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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Unit cell |
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Components
#1: Protein | Mass: 19322.172 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: VPI-5482 / Gene: BT_1677 / Production host: ![]() ![]() ![]() References: UniProt: Q8A748, ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.66 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Hepes, 30% polyethylene glycol MME 550, 40 mM magnesium chloride. Crystal dragged through Paratone prior to flash cooling, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 12, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→36.64 Å / Num. all: 50327 / Num. obs: 50327 / % possible obs: 91.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 20.25 Å2 / Rsym value: 0.061 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.79 / Num. unique all: 4618 / Rsym value: 0.432 / % possible all: 79.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3E8M Resolution: 1.8→36.64 Å / SU ML: 0.17 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 22.24 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.17 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→36.64 Å
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Refine LS restraints |
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LS refinement shell |
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