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Yorodumi- PDB-4hgo: 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hgo | |||||||||
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Title | 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase from Bacteroides thetaiotaomicron in complex with transition state mimic | |||||||||
Components | acylneuraminate cytidylyltransferase | |||||||||
Keywords | Transferase / Hydrolase / Rossmann Fold / Phosphohydroylase | |||||||||
Function / homology | Function and homology information 3-deoxy-D-glycero-D-galacto-nonulopyranosonate 9-phosphatase / N-acylneuraminate cytidylyltransferase activity / hydrolase activity, acting on ester bonds / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Daughtry, K.D. / Allen, K.N. | |||||||||
Citation | Journal: Biochemistry / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hgo.cif.gz | 143 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hgo.ent.gz | 112.6 KB | Display | PDB format |
PDBx/mmJSON format | 4hgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hgo_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4hgo_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4hgo_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 4hgo_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/4hgo ftp://data.pdbj.org/pub/pdb/validation_reports/hg/4hgo | HTTPS FTP |
-Related structure data
Related structure data | 3mmzC 3mn1C 3n07C 4hgnC 4hgpC 4hgqC 4hgrC 3e8mS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18362.064 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: VPI-5482 / Gene: BT_1713 / Plasmid: pET-3A-626 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8A712 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-VN4 / #4: Sugar | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.62 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 19% polyethylene glycol 3350 and 100 mM magnesium formate. Crystal soaked with 20 mM NaVN4 and 50 mM KDN for 1 week. Crystal dragged through Paratone prior to flash cooling, pH 7.5, VAPOR ...Details: 19% polyethylene glycol 3350 and 100 mM magnesium formate. Crystal soaked with 20 mM NaVN4 and 50 mM KDN for 1 week. Crystal 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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jul 24, 2008 / Details: Helios multi-layer optics |
Radiation | Monochromator: rotating-anode / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→28.5 Å / Num. all: 38011 / Num. obs: 38011 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 23.37 Å2 / Rsym value: 0.076 / Net I/σ(I): 6.29 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 2.73 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.485 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3E8M Resolution: 2.1→28.482 Å / SU ML: 0.28 / σ(F): 1.46 / Phase error: 25.22 / 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: 22.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→28.482 Å
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Refine LS restraints |
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LS refinement shell |
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