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- PDB-2glm: 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: 2glm | ||||||
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Title | Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) from Helicobacter pylori complexed with Compound 2 | ||||||
![]() | (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. / Liu, W. / Shen, X. / Jiang, H. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 205.6 KB | Display | ![]() |
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PDB format | ![]() | 163.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 788 KB | Display | ![]() |
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Full document | ![]() | 816.1 KB | Display | |
Data in XML | ![]() | 44.7 KB | Display | |
Data in CIF | ![]() | 61.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2gllSC ![]() 2glpC ![]() 2glvC 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: 19611.656 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q5G940, UniProt: O25928*PLUS, Lyases; Carbon-oxygen lyases; Hydro-lyases #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-BEN / #4: Chemical | ChemComp-SCB / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 0.1M Sodium Acetate trihydrate PH3.8, 2.0M Sodium Formate, 20%(w/v) Benzamidine HCl, 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: Aug 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 45511 / Num. obs: 37248 / % possible obs: 85.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 34.66 |
Reflection shell | Resolution: 2.6→2.68 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 16.03 / Num. unique all: 4426 / Rsym value: 0.077 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GLL Resolution: 2.6→50 Å / σ(F): 0
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Solvent computation | Bsol: 29.214 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.002 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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Xplor file |
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