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Yorodumi- PDB-2gll: Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gll | ||||||
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Title | Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) from Helicobacter pylori | ||||||
Components | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase | ||||||
Keywords | LYASE / FabZ | ||||||
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 / Resolution: 2.2 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gll.cif.gz | 204.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gll.ent.gz | 163.2 KB | Display | PDB format |
PDBx/mmJSON format | 2gll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gll_validation.pdf.gz | 495.9 KB | Display | wwPDB validaton report |
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Full document | 2gll_full_validation.pdf.gz | 520.4 KB | Display | |
Data in XML | 2gll_validation.xml.gz | 44.1 KB | Display | |
Data in CIF | 2gll_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/2gll ftp://data.pdbj.org/pub/pdb/validation_reports/gl/2gll | HTTPS FTP |
-Related structure data
Related structure data | 2glmC 2glpC 2glvC 1u1zS C: citing same article (ref.) 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: 19611.656 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, UniProt: O25928*PLUS, Lyases; Carbon-oxygen lyases; Hydro-lyases #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-BEN / #4: 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: 2.93 Å3/Da / Density % sol: 58.03 % |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 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: 2.2→15 Å / Num. all: 71005 / Num. obs: 69791 / % possible obs: 85.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.96 % / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.29 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.1 / Num. unique all: 6796 / Rsym value: 0.337 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U1Z Resolution: 2.2→15 Å / σ(F): 0
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Solvent computation | Bsol: 46.747 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.901 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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Xplor file |
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