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Yorodumi- PDB-4e1p: Crystal structure of the dimerization domain of Lsr2 from Mycobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e1p | ||||||
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Title | Crystal structure of the dimerization domain of Lsr2 from Mycobacterium tuberculosis in the P 1 21 1 space group | ||||||
Components | Protein lsr2 | ||||||
Keywords | DNA BINDING PROTEIN / anti-parallel beta sheet / dimer | ||||||
Function / homology | Function and homology information cellular response to oxygen levels / DNA protection / nucleoid / response to iron ion / acyltransferase activity / peptidoglycan-based cell wall / response to hydrogen peroxide / regulation of DNA-templated transcription / DNA binding / plasma membrane ...cellular response to oxygen levels / DNA protection / nucleoid / response to iron ion / acyltransferase activity / peptidoglycan-based cell wall / response to hydrogen peroxide / regulation of DNA-templated transcription / DNA binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 1.728 Å | ||||||
Authors | Summers, E.L. / Meindl, K. / Uson, I. / Arcus, V.L. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: The structure of the oligomerization domain of Lsr2 from Mycobacterium tuberculosis reveals a mechanism for chromosome organization and protection. Authors: Summers, E.L. / Meindl, K. / Uson, I. / Mitra, A.K. / Radjainia, M. / Colangeli, R. / Alland, D. / Arcus, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e1p.cif.gz | 36.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e1p.ent.gz | 25 KB | Display | PDB format |
PDBx/mmJSON format | 4e1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e1p_validation.pdf.gz | 409 KB | Display | wwPDB validaton report |
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Full document | 4e1p_full_validation.pdf.gz | 409 KB | Display | |
Data in XML | 4e1p_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 4e1p_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/4e1p ftp://data.pdbj.org/pub/pdb/validation_reports/e1/4e1p | HTTPS FTP |
-Related 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: 6539.324 Da / Num. of mol.: 2 / Fragment: dimerization domain (UNP residues 1-61) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Ra / Gene: lsr2, MT3704, MTCY07H7B.25, Rv3597c / Plasmid: pPROExHTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P65648, UniProt: P9WIP7*PLUS #2: 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: 1.9 Å3/Da / Density % sol: 35.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 26% PEG400, 0.12 M ammonium sulfate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 16, 2011 / Details: msc osmic optics |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.728→32.4 Å / Num. obs: 10538 / % possible obs: 99.4 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.728→1.82 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 6.9 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.728→29.097 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8996 / SU ML: 0.25 / σ(F): 0 / Phase error: 16.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.831 Å2 / ksol: 0.382 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 39.39 Å2 / Biso mean: 13.575 Å2 / Biso min: 3.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.728→29.097 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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