[English] 日本語
Yorodumi- PDB-3aza: Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Pla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aza | ||||||
---|---|---|---|---|---|---|---|
Title | Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Plasmodium falciparum in complex with NAS91-10 | ||||||
Components | Beta-hydroxyacyl-ACP dehydratase | ||||||
Keywords | LYASE/INHIBITOR / hot dog fold / FabZ / beta-hydroxyacyl acyl carrier protein dehydratase / Lyase / acyl carrier protein / LYASE-INHIBITOR complex | ||||||
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 | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Maity, K. / Venkata, B.S. / Kapoor, N. / Surolia, N. / Surolia, A. / Suguna, K. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2011 Title: Structural basis for the functional and inhibitory mechanisms of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Plasmodium falciparum Authors: Maity, K. / Venkata, B.S. / Kapoor, N. / Surolia, N. / Surolia, A. / Suguna, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3aza.cif.gz | 651.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3aza.ent.gz | 538.8 KB | Display | PDB format |
PDBx/mmJSON format | 3aza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/3aza ftp://data.pdbj.org/pub/pdb/validation_reports/az/3aza | HTTPS FTP |
---|
-Related structure data
Related structure data | 3az8C 3az9C 3azbC 1z6bS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17038.904 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: fabz / Plasmid: PET-28a(+)(NOVAGEN) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q965D7, Lyases; Carbon-oxygen lyases; Hydro-lyases #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-KM0 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.54 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20-25% PEG 8000, 0.1M MES, 0.1-0.3M KH2PO4, 15-20% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å | |||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 30, 2010 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 2.7→51.91 Å / Num. obs: 101381 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 61.4 Å2 / Rsym value: 0.147 / Net I/σ(I): 8.6 | |||||||||||||||
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 14780 / Rsym value: 0.508 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Z6B Resolution: 2.7→51.91 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.867 / SU B: 18.53 / SU ML: 0.345 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.01 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→51.91 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.699→2.769 Å / Total num. of bins used: 20
|