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Yorodumi- PDB-4lq2: Crystal structure of ligand binding domain of CysB, a LysR member... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lq2 | ||||||
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Title | Crystal structure of ligand binding domain of CysB, a LysR member from Salmonella typhimurium in complex with effector ligand, O-acetylserine | ||||||
Components | HTH-type transcriptional regulator CysB | ||||||
Keywords | 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 | Function and homology information cysteine biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.694 Å | ||||||
Authors | Mittal, M. / Singh, A.K. / Kumaran, S. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of ligand binding domain of CysB, a LysR member from Salmonella typhimurium in complex with effector ligand, O-acetylserine Authors: Mittal, M. / Singh, A.K. / Kumaran, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lq2.cif.gz | 59.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lq2.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 4lq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lq2_validation.pdf.gz | 445.7 KB | Display | wwPDB validaton report |
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Full document | 4lq2_full_validation.pdf.gz | 451.4 KB | Display | |
Data in XML | 4lq2_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 4lq2_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/4lq2 ftp://data.pdbj.org/pub/pdb/validation_reports/lq/4lq2 | HTTPS FTP |
-Related structure data
Related structure data | 1al3S S: Starting model for refinement |
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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: 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.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: cysB, STM1713 / Plasmid: Pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: P06614 |
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#2: Chemical | ChemComp-OAS / |
#3: 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: 2.01 Å3/Da / Density % sol: 38.76 % |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 19, 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: 2.69→50 Å / Num. obs: 5882 / % possible obs: 65.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.306 / Rsym value: 0.306 / Net I/σ(I): 35.209 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AL3 Resolution: 2.694→45.347 Å / SU ML: 0.41 / σ(F): 1.35 / Phase error: 35.89 / 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 / Bsol: 42.349 Å2 / ksol: 0.328 e/Å3 | ||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.694→45.347 Å
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Refine LS restraints |
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LS refinement shell |
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