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Yorodumi- PDB-3w7f: Crystal structure of the C(30) carotenoid dehydrosqualene synthas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w7f | |||||||||
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Title | Crystal structure of the C(30) carotenoid dehydrosqualene synthase from staphylococcus aureus complexed with farnesyl thiopyrophosphate | |||||||||
Components | Dehydrosqualene synthase4,4'-Diapophytoene synthase | |||||||||
Keywords | TRANSFERASE / CrtM / FsPP / Carotenoid biosynthesis / Staphyloxanthin biosynthesis / Head-to-head condensation | |||||||||
Function / homology | Function and homology information 4,4'-diapophytoene synthase / carotenoid biosynthetic process / farnesyltranstransferase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Liu, C.I. / Jeng, W.Y. / Wang, A.H. / Oldfield, E. | |||||||||
Citation | Journal: Science / Year: 2008 Title: A cholesterol biosynthesis inhibitor blocks Staphylococcus aureus virulence. Authors: Liu, C.I. / Liu, G.Y. / Song, Y. / Yin, F. / Hensler, M.E. / Jeng, W.Y. / Nizet, V. / Wang, A.H. / Oldfield, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w7f.cif.gz | 143.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w7f.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 3w7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/3w7f ftp://data.pdbj.org/pub/pdb/validation_reports/w7/3w7f | HTTPS FTP |
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-Related structure data
Related structure data | 2zcoSC 2zcqC 2zcrC 2zcsC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: 34787.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: ATCC 27659 / Gene: crtM / Plasmid: PET-32 XA/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21 (DE3) PLYSS / References: UniProt: A9JQL9, 4,4'-diapophytoene synthase #2: Chemical | ChemComp-FPS / #3: Chemical | ChemComp-MG / #4: 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: 2.43 Å3/Da / Density % sol: 49.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 11-21% PEG 4000, 0.3-0.4M MGCL2, 0.1M TRIS, 0.5MM FSPP, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2006 / Details: MIRRORS |
Radiation | Monochromator: NUMERICAL LINK TYPE SI(111) DOUBLE CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. all: 33078 / Num. obs: 32134 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 31.9 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3246 / % possible all: 82.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZCO Resolution: 2.25→30 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 46.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.33 Å / Rfactor Rfree error: 0.021
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