[English] 日本語
Yorodumi- PDB-3aqb: M. luteus B-P 26 heterodimeric hexaprenyl diphosphate synthase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aqb | ||||||
---|---|---|---|---|---|---|---|
Title | M. luteus B-P 26 heterodimeric hexaprenyl diphosphate synthase in complex with magnesium | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / Prenyltransferase | ||||||
Function / homology | Function and homology information hexaprenyl diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / hexaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) activity / menaquinone biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / isoprenoid biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Micrococcus luteus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å | ||||||
Authors | Sasaki, D. / Fujihashi, M. / Okuyama, N. / Kobayashi, Y. / Noike, M. / Koyama, T. / Miki, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystal structure of heterodimeric hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 reveals that the small subunit is directly involved in the product chain length regulation. Authors: Sasaki, D. / Fujihashi, M. / Okuyama, N. / Kobayashi, Y. / Noike, M. / Koyama, T. / Miki, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3aqb.cif.gz | 190.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3aqb.ent.gz | 153 KB | Display | PDB format |
PDBx/mmJSON format | 3aqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/3aqb ftp://data.pdbj.org/pub/pdb/validation_reports/aq/3aqb | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17293.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micrococcus luteus (bacteria) / Strain: B-P 26 / Gene: hexs-a / Plasmid: pET-32 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: O66127, EC: 2.5.1.33 #2: Protein | Mass: 37133.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micrococcus luteus (bacteria) / Strain: B-P 26 / Gene: hexs-b / Plasmid: pET-30 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: O66129, EC: 2.5.1.33 #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.86 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.08M Tris-HCl (pH 8.5), 0.16M Magnesium chloride hexahydrate, 24% (w/v) PEG 4000, 20% (v/v) Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→133.63 Å / Num. obs: 44225 / % possible obs: 100 % / Redundancy: 11.4 % / Rsym value: 0.083 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 5.4 / Rsym value: 0.494 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.895 / SU B: 8.993 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R Free: 0.286 / 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: 40.838 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.401→2.463 Å / Total num. of bins used: 20
|