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Yorodumi- PDB-4lon: Crystal structure of monomeric sulphate free form of ligand bindi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lon | ||||||
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Title | Crystal structure of monomeric sulphate free form of ligand binding domain of CysB,an LTTR from Salmonella typhimurium LT2 | ||||||
Components | HTH-type transcriptional regulator CysB | ||||||
Keywords | GENE REGULATION / LTTR / CysB / wHTH motif / alpha/beta fold / Rossmann fold / Transcription regulation / O-acetyl serine / N-acetyl serine binding / DNA binding | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Mittal, M. / Singh, A.K. / Kumaran, S. | ||||||
Citation | Journal: To be Published Title: Crystal structure of monomeric sulphate free form of ligand binding domain of CysB,an LTTR from Salmonella typhimurium LT2 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 | 4lon.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lon.ent.gz | 42.7 KB | Display | PDB format |
PDBx/mmJSON format | 4lon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lon_validation.pdf.gz | 432.8 KB | Display | wwPDB validaton report |
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Full document | 4lon_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 4lon_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 4lon_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/4lon ftp://data.pdbj.org/pub/pdb/validation_reports/lo/4lon | 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: 26689.342 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: 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: 1.98 Å3/Da / Density % sol: 37.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20%(w/v) PEG8000, 0.1M Sodium cacodylate pH 6.5, 0.2M magnesium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97755 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 24, 2012 / Details: mirrors |
Radiation | Monochromator: Chanel cut Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97755 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 70402 / Num. obs: 70402 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 24.542 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AL3 Resolution: 2.2→44.235 Å / SU ML: 0.17 / Isotropic thermal model: Isotropic / σ(F): 1.36 / Phase error: 29.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.098 Å2 / ksol: 0.317 e/Å3 | ||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→44.235 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: 4
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