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Yorodumi- PDB-4ea2: Crystal structure of dehydrosqualene synthase (Crtm) aureus compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ea2 | ||||||
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Title | Crystal structure of dehydrosqualene synthase (Crtm) aureus complexed with SQ-109 | ||||||
Components | Dehydrosqualene synthase4,4'-Diapophytoene synthase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / PRENYL TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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: 2.05 Å | ||||||
Authors | Lin, F.-Y. / Li, K. / Liu, Y.-L. / Oldfield, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Head-to-Head Prenyl Tranferases: Anti-Infective Drug Targets. Authors: Lin, F.Y. / Liu, Y.L. / Li, K. / Cao, R. / Zhu, W. / Axelson, J. / Pang, R. / Oldfield, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ea2.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ea2.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ea2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/4ea2 ftp://data.pdbj.org/pub/pdb/validation_reports/ea/4ea2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34361.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: crtM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A9JQL9, 4,4'-diapophytoene synthase |
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#2: Chemical | ChemComp-RWZ / |
#3: Chemical | ChemComp-SRT / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.83 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.75M POTASSIUM SODIUM TARTRATE, pH 7.4, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 2011 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 21796 / Num. obs: 21470 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Rmerge(I) obs: 0.065 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→34.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.516 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.19 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→34.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.1 Å / Total num. of bins used: 20
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