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Yorodumi- PDB-3e8m: Structure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e8m | ||||||
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Title | Structure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto-nononate-9-phosphate (KDN) Phosphatase Defines a New Clad Within the Type C0 HAD Subfamily | ||||||
Components | Acylneuraminate cytidylyltransferase | ||||||
Keywords | TRANSFERASE / 2-keto-3-deoxynononic acid 9-phosphate phosphohydrolase / Nucleotidyltransferase | ||||||
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 / SYNCHROTRON / Resolution: 1.1 Å | ||||||
Authors | Lu, Z. / Wang, L. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structure-Function Analysis of 2-Keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate Phosphatase Defines Specificity Elements in Type C0 Haloalkanoate Dehalogenase Family Members. Authors: Lu, Z. / Wang, L. / 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 | 3e8m.cif.gz | 446.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e8m.ent.gz | 373.8 KB | Display | PDB format |
PDBx/mmJSON format | 3e8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e8m_validation.pdf.gz | 509.6 KB | Display | wwPDB validaton report |
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Full document | 3e8m_full_validation.pdf.gz | 522.4 KB | Display | |
Data in XML | 3e8m_validation.xml.gz | 41 KB | Display | |
Data in CIF | 3e8m_validation.cif.gz | 62.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/3e8m ftp://data.pdbj.org/pub/pdb/validation_reports/e8/3e8m | HTTPS FTP |
-Related structure data
Related structure data | 3e81C 3e84C 1k1eS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#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 |
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-Non-polymers , 8 types, 1119 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-ACY / #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-PG4 / | #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-PGE / | #9: 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: 2.23 Å3/Da / Density % sol: 44.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% w/v polyethelene glycol (PEG) 4,000, 0.1 M Tris HCl pH 8.5, 0.2 M sodium acetate and 10 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 2, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 258326 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.2 % / Biso Wilson estimate: 8.1 Å2 / Rmerge(I) obs: 0.047 / Χ2: 0.997 / Net I/σ(I): 43.5 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.8 / Num. unique all: 22333 / Χ2: 1.011 / % possible all: 84.8 |
-Processing
Software |
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Refinement | Starting model: pdb entry 1K1E Resolution: 1.1→28.782 Å / Occupancy max: 1 / Occupancy min: 0.13 / SU ML: 0.09 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 1.89 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.109 Å2 / ksol: 0.41 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.45 Å2 / Biso mean: 17.685 Å2 / Biso min: 8.24 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.1→28.782 Å
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Refine LS restraints |
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LS refinement shell |
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