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- PDB-3doy: Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3doy | ||||||
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Title | Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with compound 3i | ||||||
![]() | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase | ||||||
![]() | LYASE / FabZ complex | ||||||
Function / homology | ![]() (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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, L. / He, L. / Liu, X. / Liu, H. / Shen, X. / Jiang, H. | ||||||
![]() | ![]() Title: Discovering potent inhibitors against the beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Helicobacter pylori: structure-based design, synthesis, bioassay, and crystal structure determination. Authors: He, L. / Zhang, L. / Liu, X. / Li, X. / Zheng, M. / Li, H. / Yu, K. / Chen, K. / Shen, X. / Jiang, H. / Liu, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.7 KB | Display | ![]() |
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PDB format | ![]() | 158.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3dozC ![]() 3dp0C ![]() 3dp1C ![]() 3dp2C ![]() 3dp3C ![]() 2gllS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() References: UniProt: Q5G940, Lyases; Carbon-oxygen lyases; Hydro-lyases #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-BEN / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.21 % |
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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 Additive, 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: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 11, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 53457 / % possible obs: 96.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.8 / Num. unique all: 37945 / Rsym value: 0.367 / % possible all: 94.6 |
-Phasing
Phasing | Method: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MR | Rfactor: 0.449 / Cor.coef. Fo:Fc: 0.579
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Phasing dm shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GLL Resolution: 2.4→15 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 37.891 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.19 Å2 / Biso mean: 19.445 Å2 / Biso min: 5.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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Xplor file |
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