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- PDB-4lq5: Crystal structure of ligand binding domain of CysB, a LysR member... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lq5 | ||||||
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Title | Crystal structure of ligand binding domain of CysB, a LysR member from Salmonella typhimurium LT2 in complex with effector ligand, O-acetylserine at 2.8A | ||||||
![]() | HTH-type transcriptional regulator CysB | ||||||
![]() | GENE REGULATION / wHTH motif/ PBP type II alpha/beta fold / Rossmann fold / LTTR / Transcriptional Regulation / O-acetyl serine / N-acetyl serine binding / DNA binding / Cytoplasmic | ||||||
Function / homology | ![]() cysteine biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mittal, M. / Singh, A.K. / Kumaran, S. | ||||||
![]() | ![]() Title: rystal structure of ligand binding domain of CysB, a LysR member from Salmonella typhimurium LT2 in complex with effector ligand, O-acetylserine at 2.8A Authors: Mittal, M. / Singh, A.K. / Kumaran, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.9 KB | Display | ![]() |
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PDB format | ![]() | 43.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.3 KB | Display | ![]() |
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Full document | ![]() | 456.5 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1al3S S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 27518.223 Da / Num. of mol.: 1 / Fragment: UNP residues 86-324 Source method: isolated from a genetically manipulated source Details: IPTG Inducible Source: (gene. exp.) ![]() Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: cysB, STM1713 / Plasmid: Pet28a / Production host: ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30%(w/v) PEG4000, 0.1M Tris pH 8.5, 0.2M Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 18, 2013 |
Radiation | Monochromator: Graphite polar / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 18561 / Num. obs: 18561 / % possible obs: 52.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.223 / Rsym value: 0.223 / Net I/σ(I): 18.634 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1AL3 Resolution: 2.803→41.845 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.803→41.845 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
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