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Yorodumi- PDB-3tfp: Crystal Structure of Dehydrosqualene Synthase (CrtM) from S. aure... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tfp | ||||||
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Title | Crystal Structure of Dehydrosqualene Synthase (CrtM) from S. aureus Complexed with BPH-1162 | ||||||
Components | Dehydrosqualene synthase4,4'-Diapophytoene synthase | ||||||
Keywords | TRANSFERASE/transferase inhibitor / Head-to-Head Prenyl Synthase / 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 Å | ||||||
Authors | Lin, F.-Y. / Liu, Y.-L. / Zhang, Y. / Oldfield, E. | ||||||
Citation | Journal: Chemmedchem / Year: 2012 Title: Dual dehydrosqualene/squalene synthase inhibitors: leads for innate immune system-based therapeutics. Authors: Lin, F.Y. / Zhang, Y. / Hensler, M. / Liu, Y.L. / Chow, O.A. / Zhu, W. / Wang, K. / Pang, R. / Thienphrapa, W. / 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 | 3tfp.cif.gz | 79.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tfp.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 3tfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/3tfp ftp://data.pdbj.org/pub/pdb/validation_reports/tf/3tfp | HTTPS FTP |
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-Related structure data
Related structure data | 3tfnC 3tfvC 2zcqS 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: 34787.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: crtM / Plasmid: pET32-LIC / Production host: Escherichia coli (E. coli) References: UniProt: A9JQL9, Transferases; Transferring alkyl or aryl groups, other than methyl groups | ||||
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#2: Chemical | #3: Chemical | ChemComp-03L / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.2M Potassium sodium tartrate, 20% w/v PEG 3350, 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-F / Wavelength: 0.9 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. all: 26359 / Num. obs: 26333 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 35.9 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2.3 / % possible all: 99 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.6.4_486) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZCQ Resolution: 2→28.106 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.986 Å2 / ksol: 0.329 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→28.106 Å
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Refine LS restraints |
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LS refinement shell |
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