[English] 日本語
Yorodumi- PDB-2z6i: Crystal Structure of S. pneumoniae Enoyl-Acyl Carrier Protein Red... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z6i | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of S. pneumoniae Enoyl-Acyl Carrier Protein Reductase (FabK) | ||||||
Components | Trans-2-enoyl-ACP reductase II | ||||||
Keywords | OXIDOREDUCTASE / FATTY ACID SYNTHESIS / ANTIBIOTICS / FLAVOPROTEIN | ||||||
Function / homology | Function and homology information nitronate monooxygenase / Oxidoreductases; Acting on the CH-CH group of donors / nitronate monooxygenase activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Saito, J. / Yamada, M. / Watanabe, T. / Takeuchi, Y. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Crystal structure of enoyl-acyl carrier protein reductase (FabK) from Streptococcus pneumoniae reveals the binding mode of an inhibitor. Authors: Saito, J. / Yamada, M. / Watanabe, T. / Iida, M. / Kitagawa, H. / Takahata, S. / Ozawa, T. / Takeuchi, Y. / Ohsawa, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2z6i.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2z6i.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 2z6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z6i_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2z6i_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2z6i_validation.xml.gz | 28 KB | Display | |
Data in CIF | 2z6i_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z6i ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z6i | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35758.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: fabK / Plasmid: pET-21b(+) / Production host: Escherichia coli (E. coli) References: UniProt: Q9FBC5, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-MPD / ( | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.51 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 8-15% PEG 1000, 8-15% MPD, 0.1M MES pH 5.5-7.0, 0.1M ammonium chloride, 0.2M calcium chloride, 5mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 0.90000, 0.97888, 0.97932 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 3, 2004 Details: A fixed exit Si double crystal monochromator followed byStandard double crystal monochromator and Rh-coated downward-deflection mirror with a typical glancing angle of 3.7mrad | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 1.7→29.14 Å / Num. obs: 68157 / % possible obs: 99.8 % / Redundancy: 4.3 % / Biso Wilson estimate: 17.183 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.8 | ||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 4.3 / % possible all: 99.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.7→29.14 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.345 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.61 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→29.14 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
|