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Yorodumi- PDB-4f6x: Crystal structure of dehydrosqualene synthase (crtm) from s. aure... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f6x | ||||||
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Title | Crystal structure of dehydrosqualene synthase (crtm) from s. aureus complexed with bph-1112 | ||||||
Components | Dehydrosqualene synthase4,4'-Diapophytoene synthase | ||||||
Keywords | TRANSFERASE/TRANSFERASE inhibitor / DEHYDROSQUALENE SYNTHASE / VIRULENCE FACTOR / BPH-1112 / 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: 1.98 Å | ||||||
Authors | Lin, F.-Y. / Zhang, Y. / Liu, Y.-L. / Oldfield, E. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2012 Title: HIV-1 Integrase Inhibitor-Inspired Antibacterials Targeting Isoprenoid Biosynthesis. Authors: Zhang, Y. / Lin, F.-Y. / Li, K. / Zhu, W. / Liu, Y.L. / Cao, R. / Pang, R. / Lee, E. / Axelson, J. / Hensler, M. / Wang, K. / Molohon, K.J. / Wang, Y. / Mitchell, D.A. / Nizet, V. / Oldfield, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f6x.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f6x.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 4f6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/4f6x ftp://data.pdbj.org/pub/pdb/validation_reports/f6/4f6x | HTTPS FTP |
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-Related structure data
Related structure data | 3th8C 4f6vC 2zcoS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34716.418 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-ZYL / | ||||
#3: Chemical | #4: Chemical | ChemComp-TAR / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.75M POTASSIUM SODIUM TARTRATE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 11, 2010 |
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: 1.91→50 Å / Num. obs: 27055 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.072 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZCO Resolution: 1.98→26.25 Å / SU ML: 0.2 / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.91 Å2 / ksol: 0.37 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→26.25 Å
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Refine LS restraints |
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LS refinement shell |
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