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Yorodumi- PDB-4lp2: Crystal structure of monomeric ligand binding domain of S. typhim... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lp2 | ||||||
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Title | Crystal structure of monomeric ligand binding domain of S. typhimurium CysB, a LysR transcriptional regulator at 2.2A | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Mittal, M. / Singh, A.K. / Kumaran, S. | ||||||
Citation | Journal: To be Published Title: Crystal structure of monomeric ligand binding domain of S. typhimurium CysB, a LysR transcriptional regulator at 2.2A 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 | 4lp2.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lp2.ent.gz | 43.1 KB | Display | PDB format |
PDBx/mmJSON format | 4lp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lp2_validation.pdf.gz | 422.8 KB | Display | wwPDB validaton report |
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Full document | 4lp2_full_validation.pdf.gz | 433.9 KB | Display | |
Data in XML | 4lp2_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 4lp2_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/4lp2 ftp://data.pdbj.org/pub/pdb/validation_reports/lp/4lp2 | 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 on special symmetry positions |
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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: 2 Å3/Da / Density % sol: 38.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M imidazole pH 6.5, 1.0M Sodium acetate, 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: Jul 14, 2011 |
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: 2.3→40 Å / Num. all: 30862 / Num. obs: 30862 / % possible obs: 78.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.178 / Rsym value: 0.178 / Net I/σ(I): 32.974 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AL3 Resolution: 2.3→26.427 Å / SU ML: 0.3 / Isotropic thermal model: isotrpic / σ(F): 0 / Phase error: 31.81 / 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: 2.3→26.427 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: 3
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