[English] 日本語
Yorodumi- PDB-3hsq: Structural Basis for the Sugar Nucleotide and Acyl Chain Selectiv... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hsq | ||||||
---|---|---|---|---|---|---|---|
Title | Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira interrogans LpxA | ||||||
Components | Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase | ||||||
Keywords | TRANSFERASE / L.interrogans LPXA / LPXA / LPXA crystal structure / Acyltransferase / Lipid A biosynthesis / Lipid synthesis | ||||||
Function / homology | Function and homology information acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity / lipid A biosynthetic process Similarity search - Function | ||||||
Biological species | Leptospira interrogans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Robins, L.I. / Williams, A.H. / Raetz, C.R. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural basis for the sugar nucleotide and acyl-chain selectivity of Leptospira interrogans LpxA. Authors: Robins, L.I. / Williams, A.H. / Raetz, C.R. | ||||||
History |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3hsq.cif.gz | 166.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3hsq.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/3hsq ftp://data.pdbj.org/pub/pdb/validation_reports/hs/3hsq | HTTPS FTP |
---|
-Related structure data
Related structure data | 3i3aC 3i3xC 1lxaS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
2 |
| |||||||||
3 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 28202.086 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira interrogans (bacteria) / Strain: K-12 / Gene: LA3949, LA_3949, lpxA / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: Q8EZA6, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.55 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% isopropanol, 1M sodium citrate, 20% polyethylene glycol 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 15, 2006 |
Radiation | 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→26.36 Å / Num. obs: 44733 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LXA Resolution: 2.1→26.36 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.57 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.382 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→26.36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
|