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Yorodumi- PDB-5h9d: Crystal structure of Heptaprenyl Diphosphate Synthase from Staphy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h9d | ||||||
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Title | Crystal structure of Heptaprenyl Diphosphate Synthase from Staphylococcus aureus | ||||||
Components |
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Keywords | TRANSFERASE / metal-binding / substrate binding / acidocalcisomal pyrophosphatase | ||||||
Function / homology | Function and homology information heptaprenyl diphosphate synthase activity => GO:0000010 / heptaprenyl diphosphate synthase / dimethylallyltranstransferase / prenyltransferase activity / menaquinone biosynthetic process / isoprenoid biosynthetic process / dimethylallyltranstransferase activity Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.68 Å | ||||||
Authors | Wei, H.L. / Liu, W.D. / Zheng, Y.Y. / Ko, T.P. / Chen, C.C. / Guo, R.T. | ||||||
Citation | Journal: ChemMedChem / Year: 2016 Title: Structure, Function, and Inhibition of Staphylococcus aureus Heptaprenyl Diphosphate Synthase Authors: Desai, J. / Liu, Y.L. / Wei, H. / Liu, W. / Ko, T.P. / Guo, R.T. / Oldfield, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h9d.cif.gz | 218.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h9d.ent.gz | 176.6 KB | Display | PDB format |
PDBx/mmJSON format | 5h9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h9d_validation.pdf.gz | 488.6 KB | Display | wwPDB validaton report |
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Full document | 5h9d_full_validation.pdf.gz | 548.5 KB | Display | |
Data in XML | 5h9d_validation.xml.gz | 44.9 KB | Display | |
Data in CIF | 5h9d_validation.cif.gz | 61.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/5h9d ftp://data.pdbj.org/pub/pdb/validation_reports/h9/5h9d | HTTPS FTP |
-Related structure data
Similar structure data |
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-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36199.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: hepT, gerCC, AFO87_08490, AL078_00755, AL493_08930, AL498_03950, AL508_07350, AM595_07380, CH51_07695, EQ80_006970, ER12_006960, ERS092844_00891, ERS093009_01199, ERS195423_01812, ERS365775_ ...Gene: hepT, gerCC, AFO87_08490, AL078_00755, AL493_08930, AL498_03950, AL508_07350, AM595_07380, CH51_07695, EQ80_006970, ER12_006960, ERS092844_00891, ERS093009_01199, ERS195423_01812, ERS365775_02304, ERS410449_02217, ERS411009_00914, ERS411017_01500, ERS445052_01888, FE68_02720, RL02_11030, RT87_07355, SAMI_1402 Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0D6HKK2, UniProt: Q2FYG6*PLUS, dimethylallyltranstransferase, heptaprenyl diphosphate synthase #2: Protein | Mass: 22185.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: AL078_00765, AM595_07390, AUC48_07185, AUC49_07360, AUC50_07510, BN1321_260110, ERS179246_00728, ERS445051_01360, NI36_07270, RT87_07365, SA7112_09025, SAFDA_1366, SAMI_1404, SASCBU26_01375 Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: W8TTD5 #3: Protein/peptide | Mass: 2093.390 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: W8TTD5, UniProt: Q2FYG4*PLUS #4: Chemical | ChemComp-PO4 / #5: 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: 2.92 Å3/Da / Density % sol: 57.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: Citic acid, bis-tris propane, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.68→25 Å / Num. obs: 35313 / % possible obs: 92 % / Redundancy: 5 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.025 / Rrim(I) all: 0.057 / Χ2: 2.258 / Net I/av σ(I): 38.038 / Net I/σ(I): 25 / Num. measured all: 175144 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→25 Å / Cross valid method: FREE R-VALUE / σ(F): 0 Details: Chains K/L are built from residual densities exist between the neighboring heterodimers. Author persume Chains K/L come from a neighboring heterodimer with the region 140-170 of the protein unfolded.
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Solvent computation | Bsol: 50.3455 Å2 | ||||||||||||||||||||
Displacement parameters | Biso max: 148.41 Å2 / Biso mean: 75.7839 Å2 / Biso min: 37.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.68→25 Å
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Refine LS restraints |
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