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Open data
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Basic information
Entry | Database: PDB / ID: 1rfy | ||||||
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Title | Crystal Structure of Quorum-Sensing Antiactivator TraM | ||||||
![]() | Transcriptional repressor traM | ||||||
![]() | TRANSCRIPTION / inter- and intra-molcular two-helix coiled coil / homodimer | ||||||
Function / homology | Transcriptional repressor TraM / Transcriptional repressor TraM superfamily / Prokaryotic Transcriptional repressor TraM / HR1 repeat / Helix Hairpins / negative regulation of DNA-templated transcription / Orthogonal Bundle / Mainly Alpha / Transcriptional repressor TraM![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, G. / Malenkos, J.W. / Cha, M.R. / Fuqua, C. / Chen, L. | ||||||
![]() | ![]() Title: Quorum-sensing antiactivator TraM forms a dimer that dissociates to inhibit TraR Authors: Chen, G. / Malenkos, J.W. / Cha, M.R. / Fuqua, C. / Chen, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.6 KB | Display | ![]() |
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PDB format | ![]() | 36.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422 KB | Display | ![]() |
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Full document | ![]() | 422.8 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | the second protomer of the biological assembly is generated by the two-fold axis: 2-x, 1-y, z the second protomer of the biological assembly is generated by the two-fold axis: 1.5-x, 0.5-y, z |
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Components
#1: Protein | Mass: 11365.187 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: amonium acetate, sodium citrate, PEG 2000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 17, 2003 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9636 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→60 Å / Num. all: 30102 / Num. obs: 29690 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 9.9 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 37.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1234 / % possible all: 84.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.2428 Å2 / ksol: 0.392037 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→60 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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