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Yorodumi- PDB-4e1r: Crystal structure of the dimerization domain of Lsr2 from Mycobac... -
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-Basic information
Entry | Database: PDB / ID: 4e1r | ||||||
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Title | Crystal structure of the dimerization domain of Lsr2 from Mycobacterium tuberculosis in the P 31 2 1 space group | ||||||
Components | Protein lsr2 | ||||||
Keywords | DNA BINDING PROTEIN / anti-parallel beta sheet / dimer | ||||||
Function / homology | Function and homology information DNA protection / cellular response to oxygen levels / nucleoid / response to iron ion / acyltransferase activity / peptidoglycan-based cell wall / response to hydrogen peroxide / regulation of DNA-templated transcription / DNA binding / plasma membrane ...DNA protection / cellular response to oxygen levels / nucleoid / response to iron ion / acyltransferase activity / peptidoglycan-based cell wall / response to hydrogen peroxide / regulation of DNA-templated transcription / DNA binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.041 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 | 4e1r.cif.gz | 37.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e1r.ent.gz | 24.6 KB | Display | PDB format |
PDBx/mmJSON format | 4e1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e1r_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
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Full document | 4e1r_full_validation.pdf.gz | 432.1 KB | Display | |
Data in XML | 4e1r_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 4e1r_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/4e1r ftp://data.pdbj.org/pub/pdb/validation_reports/e1/4e1r | HTTPS FTP |
-Related structure data
Related structure data | 4e1pSC S: Starting model for refinement C: citing same article (ref.) |
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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: 9641.638 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: 2.6 Å3/Da / Density % sol: 52.62 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.01 M cobalt(II) chloride, 1.4 M ammonium sulfate, 0.1 M MES, pH 6.5, 7.5% 1,4-dioxane, 0.2% w/v trypsin, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9786 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 27, 2011 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.041→52.655 Å / Num. obs: 13341 / Redundancy: 20.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.041→2.15 Å / Redundancy: 20.5 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 6.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4E1P Resolution: 2.041→36.143 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7514 / SU ML: 0.48 / σ(F): 0 / Phase error: 30.47 / 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: 36.635 Å2 / ksol: 0.344 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.88 Å2 / Biso mean: 36.6759 Å2 / Biso min: 20.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.041→36.143 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: 9
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