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- PDB-6ko7: Crystal structure of the Ethidium bound RamR determined with XtaL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ko7 | ||||||
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Title | Crystal structure of the Ethidium bound RamR determined with XtaLAB Synergy | ||||||
![]() | Putative regulatory protein | ||||||
![]() | DNA BINDING PROTEIN / multisite binding pocket / HTH-MOTIF | ||||||
Function / homology | ![]() transcription cis-regulatory region binding / DNA-binding transcription factor activity / RNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
Model details | framework as crystalline sponge method | ||||||
![]() | Matsumoto, T. / Nakashima, R. / Yamano, A. / Nishino, K. | ||||||
![]() | ![]() Title: Development of a structure determination method using a multidrug-resistance regulator protein as a framework. Authors: Matsumoto, T. / Nakashima, R. / Yamano, A. / Nishino, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 318.8 KB | Display | ![]() |
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PDB format | ![]() | 259.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 46 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ko8C ![]() 6ko9C ![]() 3vvyS S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 22044.262 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 14028s / SGSC 2262 / Gene: STM14_0676 / Plasmid: PET DUET / Production host: ![]() ![]() #2: Chemical | ChemComp-ET / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.3 % / Mosaicity: 0.85 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG3350, ammonium sulfate, sodium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU HyPic-6000HE / Detector: PIXEL / Date: Sep 15, 2016 |
Radiation | Monochromator: multi-layer mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→23.45 Å / Num. obs: 88793 / % possible obs: 98.7 % / Redundancy: 2.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.047 / Rrim(I) all: 0.084 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.402 / Num. unique obs: 4303 / CC1/2: 0.479 / Rpim(I) all: 0.371 / Rrim(I) all: 0.548 / % possible all: 94.8 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3VVY Resolution: 1.7→23.45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.82 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.111 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.73 Å2 / Biso mean: 25.753 Å2 / Biso min: 12.72 Å2
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Refinement step | Cycle: final / Resolution: 1.7→23.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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