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Yorodumi- PDB-4gwo: Crystal structure of ligand binding domain of LysR family member,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gwo | ||||||
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Title | Crystal structure of ligand binding domain of LysR family member,CysB in complex with sulfate from Salmonella typhimurium LT2 | ||||||
Components | HTH-type transcriptional regulator CysB | ||||||
Keywords | GENE REGULATION / LTTR / CysB / Sulfate / alpha/beta fold / Transcription regulation / 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 TYPHIMURIUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.394 Å | ||||||
Authors | Mittal, M. / Singh, A.K. / Kumaran, S. | ||||||
Citation | Journal: To be Published Title: Crystal structure of ligand binding domain of LysR family member,CysB in complex with sulfate 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 | 4gwo.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gwo.ent.gz | 82.2 KB | Display | PDB format |
PDBx/mmJSON format | 4gwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gwo_validation.pdf.gz | 463.5 KB | Display | wwPDB validaton report |
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Full document | 4gwo_full_validation.pdf.gz | 472.7 KB | Display | |
Data in XML | 4gwo_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 4gwo_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/4gwo ftp://data.pdbj.org/pub/pdb/validation_reports/gw/4gwo | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 36886.000 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, UNP residues 86-324 Source method: isolated from a genetically manipulated source Details: IPTG inducible / Source: (gene. exp.) SALMONELLA 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 #2: Chemical | ChemComp-GOL / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30%(w/v) PEG5000 MME,0.2M ammonium sulphate, 0.1M MES, pH 6.5, 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: Jun 18, 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: 2.394→45.71 Å / Num. all: 47731 / Num. obs: 17828 / % possible obs: 67.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 38.14 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AL3 Resolution: 2.394→26.325 Å / SU ML: 0.35 / Isotropic thermal model: Isotropic / σ(F): 1.36 / Phase error: 32.29 / Stereochemistry target values: ML Details: DURING CRYSTALLIZATION, CYSB N-TERMINAL DOMAIN CLEAVED AND COULD NOT BE FOUND WHEN RUNNING IN THE GEL.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.394→26.325 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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