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Yorodumi- PDB-3aqc: M. luteus B-P 26 heterodimeric hexaprenyl diphosphate synthase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aqc | ||||||
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Title | M. luteus B-P 26 heterodimeric hexaprenyl diphosphate synthase in complex with magnesium and FPP analogue | ||||||
Components |
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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 / FOURIER SYNTHESIS / Resolution: 2.61 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aqc.cif.gz | 191.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aqc.ent.gz | 153.7 KB | Display | PDB format |
PDBx/mmJSON format | 3aqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/3aqc ftp://data.pdbj.org/pub/pdb/validation_reports/aq/3aqc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#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 |
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-Non-polymers , 4 types, 78 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: 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: 2.62 Å3/Da / Density % sol: 53 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→133.63 Å / Num. obs: 34831 / % possible obs: 100 % / Redundancy: 15.9 % / Rsym value: 0.099 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 9.1 / Rsym value: 0.342 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.61→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.876 / SU B: 11.944 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 46.323 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.61→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.606→2.673 Å / Total num. of bins used: 20
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