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Yorodumi- PDB-4a0x: Structure of the global transcription regulator FapR from Staphyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a0x | ||||||
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Title | Structure of the global transcription regulator FapR from Staphylococcus aureus | ||||||
Components | TRANSCRIPTION FACTOR FAPR | ||||||
Keywords | TRANSCRIPTION / LIPID HOMEOSTASIS | ||||||
Function / homology | Function and homology information negative regulation of fatty acid biosynthetic process / fatty acid biosynthetic process / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Albanesi, D. / Guerin, M.E. / Buschiazzo, A. / de Mendoza, D. / Alzari, P.M. | ||||||
Citation | Journal: Plos Pathog. / Year: 2013 Title: Structural Basis for Feed-Forward Transcriptional Regulation of Membrane Lipid Homeostasis in Staphylococcus Aureus. Authors: Albanesi, D. / Reh, G. / Guerin, M.E. / Schaeffer, F. / Debarbouille, M. / Buschiazzo, A. / Schujman, G.E. / De Mendoza, D. / Alzari, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a0x.cif.gz | 89.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a0x.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 4a0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/4a0x ftp://data.pdbj.org/pub/pdb/validation_reports/a0/4a0x | HTTPS FTP |
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-Related structure data
Related structure data | 4a0yC 4a0zC 4a12C 2f3xS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 22026.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: D6UB50, UniProt: Q2FZ56*PLUS | ||||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-MES / | #5: 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: 3.8 Å3/Da / Density % sol: 67 % / Description: NONE |
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Crystal grow | pH: 5.4 / Details: 6% PEG-8000, 0.1M MES, 0.2 M ZN ACETATE, PH 5.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 16, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47 Å / Num. obs: 12145 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2F3X Resolution: 2.4→78.09 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.513 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.212 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.009 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→78.09 Å
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Refine LS restraints |
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