[English] 日本語
Yorodumi- PDB-4a12: Structure of the global transcription regulator FapR from Staphyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a12 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the global transcription regulator FapR from Staphylococcus aureus in complex with DNA operator | ||||||
Components |
| ||||||
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) BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4a12.cif.gz | 407.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4a12.ent.gz | 333.5 KB | Display | PDB format |
PDBx/mmJSON format | 4a12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a12_validation.pdf.gz | 465.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4a12_full_validation.pdf.gz | 478.6 KB | Display | |
Data in XML | 4a12_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 4a12_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/4a12 ftp://data.pdbj.org/pub/pdb/validation_reports/a1/4a12 | HTTPS FTP |
-Related structure data
Related structure data | 4a0xSC 4a0yC 4a0zC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22120.135 Da / Num. of mol.: 4 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 #2: DNA chain | | Mass: 12195.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) BACILLUS SUBTILIS (bacteria) / References: GenBank: 320017650 #3: DNA chain | | Mass: 12423.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) BACILLUS SUBTILIS (bacteria) / References: GenBank: 320017650 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.7 Å3/Da / Density % sol: 75 % / Description: NONE |
---|---|
Crystal grow | Details: 3.2 M SODIUM FORMATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→35 Å / Num. obs: 44060 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 16 % / Biso Wilson estimate: 83.11 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 3.15→3.32 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.4 / % possible all: 93.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4A0X Resolution: 3.15→31.75 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.9228 / SU R Cruickshank DPI: 0.445 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.429 / SU Rfree Blow DPI: 0.259 / SU Rfree Cruickshank DPI: 0.265
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 114.42 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.745 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→31.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.15→3.23 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|