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Yorodumi- PDB-3ed0: Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ed0 | ||||||
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Title | Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with emodin | ||||||
Components | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase | ||||||
Keywords | LYASE / FabZ complex / Emodin / Cytoplasm / Lipid A biosynthesis / Lipid synthesis | ||||||
Function / homology | Function and homology information (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / lipid A biosynthetic process / fatty acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Zhang, L. / Zhang, H. / Liu, W. / Guo, Y. / Shen, X. / Jiang, H. | ||||||
Citation | Journal: BMC MICROBIOL. / Year: 2009 Title: Emodin targets the beta-hydroxyacyl-acyl carrier protein dehydratase from Helicobacter pylori: enzymatic inhibition assay with crystal structural and thermodynamic characterization Authors: Chen, J. / Zhang, L. / Zhang, Y. / Zhang, H. / Du, J. / Ding, J. / Guo, Y. / Jiang, H. / Shen, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ed0.cif.gz | 200.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ed0.ent.gz | 159.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ed0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ed0_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3ed0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3ed0_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 3ed0_validation.cif.gz | 57.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/3ed0 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/3ed0 | HTTPS FTP |
-Related structure data
Related structure data | 2gllS S: Starting model for refinement |
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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
#1: Protein | ( Mass: 18206.119 Da / Num. of mol.: 6 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, Lyases; Carbon-oxygen lyases; Hydro-lyases #2: Chemical | ChemComp-BEN / #3: Chemical | ChemComp-CL / #4: Chemical | #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: 3.18 Å3/Da / Density % sol: 61.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 0.1M Sodium Acetate trihydrate, 2.0M Sodium Formate, 20%(w/v) Benzamidine HCl, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→93.25 Å / Num. obs: 62492 / % possible obs: 99.6 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 5.717 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GLL Resolution: 2.3→20 Å / Occupancy max: 1 / Occupancy min: 0.8 / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 67.75 Å2 / Biso mean: 24.596 Å2 / Biso min: 9.25 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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