[English] 日本語
Yorodumi- PDB-2glv: Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2glv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) mutant(Y100A) from Helicobacter pylori | ||||||
Components | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase | ||||||
Keywords | LYASE / FabZ mutant | ||||||
Function / homology | Function and homology information (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / lipid A biosynthetic process / fatty acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zhang, L. / Liu, W. / Shen, X. / Jiang, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structural basis for catalytic and inhibitory mechanisms of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ). Authors: Zhang, L. / Liu, W. / Hu, T. / Du, L. / Luo, C. / Chen, K. / Shen, X. / Jiang, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2glv.cif.gz | 363.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2glv.ent.gz | 297.7 KB | Display | PDB format |
PDBx/mmJSON format | 2glv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/2glv ftp://data.pdbj.org/pub/pdb/validation_reports/gl/2glv | HTTPS FTP |
---|
-Related structure data
Related structure data | 2gllSC 2glmC 2glpC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | ( Mass: 19519.559 Da / Num. of mol.: 12 / Mutation: Y100A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: SS1 / Gene: FabZ / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 References: UniProt: Q5G940, UniProt: O25928*PLUS, Lyases; Carbon-oxygen lyases; Hydro-lyases #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.15 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 0.1M Sodium Acetate trihydrate PH5.8, 2.0M Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 10, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 76473 / Num. obs: 76177 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Χ2: 1.196 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible obs: 94.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 4.12 / Num. unique all: 7381 / Num. unique obs: 7381 / Rsym value: 0.283 / Χ2: 0.904 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GLL Resolution: 2.5→50 Å / σ(F): 0
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 53.82 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.422 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
|