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Yorodumi- PDB-1hw2: FADR-DNA COMPLEX: TRANSCRIPTIONAL CONTROL OF FATTY ACID METABOLIS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hw2 | ||||||
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Title | FADR-DNA COMPLEX: TRANSCRIPTIONAL CONTROL OF FATTY ACID METABOLISM IN ECHERICHIA COLI | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / helix-turn-helix / helix bundle / protein-DNA complex / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information fatty-acyl-CoA binding / regulation of fatty acid metabolic process / positive regulation of fatty acid biosynthetic process / fatty acid metabolic process / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Xu, Y. / Heath, R.J. / Li, Z. / Rock, C.O. / White, S.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: The FadR.DNA complex. Transcriptional control of fatty acid metabolism in Escherichia coli. Authors: Xu, Y. / Heath, R.J. / Li, Z. / Rock, C.O. / White, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hw2.cif.gz | 121.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hw2.ent.gz | 91.6 KB | Display | PDB format |
PDBx/mmJSON format | 1hw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/1hw2 ftp://data.pdbj.org/pub/pdb/validation_reports/hw/1hw2 | 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: DNA chain | Mass: 6728.341 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 6777.379 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 27002.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FADR / Plasmid: PPJ139 / Production host: Escherichia coli (E. coli) / Strain (production host): UB1005 / References: UniProt: P0A8V6 #4: Chemical | ChemComp-MG / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.41 Å3/Da / Density % sol: 72.12 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: evaporation / pH: 6 Details: isopropanol, MES, magnesium chloride, pH 6.0, EVAPORATION, temperature 290.0K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9537 Å |
Detector | Detector: CCD / Date: Sep 2, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→40 Å / Num. all: 643902 / Num. obs: 20310 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.2→3.31 Å / Rmerge(I) obs: 0.346 / % possible all: 99.6 |
Reflection | *PLUS Num. measured all: 643902 |
Reflection shell | *PLUS % possible obs: 99.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Native FadR dimer Resolution: 3.25→40 Å / Isotropic thermal model: grouped-B / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 70.6 Å2
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Refinement step | Cycle: LAST / Resolution: 3.25→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.25→3.37 Å
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.235 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 70.6 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.358 |