+Open data
-Basic information
Entry | Database: PDB / ID: 3lsr | ||||||
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Title | Crystal structure of DesT in complex with duplex DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / Transcriptional Repressor / DesT-DNA complex / TetR family / DNA-binding / Transcription / Transcription regulation / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information DNA-binding transcription repressor activity / negative regulation of fatty acid metabolic process / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Miller, D.J. / White, S.W. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Structural basis for the transcriptional regulation of membrane lipid homeostasis. Authors: Miller, D.J. / Zhang, Y.M. / Subramanian, C. / 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 | 3lsr.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lsr.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 3lsr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lsr_validation.pdf.gz | 442.6 KB | Display | wwPDB validaton report |
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Full document | 3lsr_full_validation.pdf.gz | 446.6 KB | Display | |
Data in XML | 3lsr_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 3lsr_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/3lsr ftp://data.pdbj.org/pub/pdb/validation_reports/ls/3lsr | HTTPS FTP |
-Related structure data
Related structure data | 3lsjC 3lspSC 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: 24000.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: desT, PA4890 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9HUS3 | ||
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#2: DNA chain | Mass: 10145.531 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Chemical | #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: 3.35 Å3/Da / Density % sol: 63.3 % |
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Crystal grow | Temperature: 291 K / Method: grown under mineral oil / pH: 7 Details: ML- 0.1M Mes pH7.0, 9% PEG 20K. Protein sample- 0.3 mM protein, 0.3 mM oligo, 0.3 mM 18:1delta9-CoA. Drop- 2ul ML + 2 ul protein + 0.5 uL 1M ammonium sulfate., grown under mineral oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 11, 2008 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 15465 / Num. obs: 14862 / % possible obs: 96.1 % / Redundancy: 7 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 40.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 3LSP Resolution: 2.55→41.38 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.901 / SU B: 10.223 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.367 / ESU R Free: 0.269 / 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: 61.408 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→41.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.616 Å / Total num. of bins used: 20
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