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- PDB-4e1p: Crystal structure of the dimerization domain of Lsr2 from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 4e1p
TitleCrystal structure of the dimerization domain of Lsr2 from Mycobacterium tuberculosis in the P 1 21 1 space group
ComponentsProtein lsr2
KeywordsDNA 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 / cytoplasm / cytosol
Similarity search - Function
Lsr2, dimerisation domain / Lsr2 / Lsr2, dimerization domain / : / Lsr2 dimerization domain / Lsr2 DNA-binding domain / E3-binding domain superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoid-associated protein Lsr2 / Nucleoid-associated protein Lsr2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 1.728 Å
AuthorsSummers, E.L. / Meindl, K. / Uson, I. / Arcus, V.L.
CitationJournal: 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
DepositionMar 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein lsr2
B: Protein lsr2


Theoretical massNumber of molelcules
Total (without water)13,0792
Polymers13,0792
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-16 kcal/mol
Surface area6790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.510, 27.030, 56.830
Angle α, β, γ (deg.)90.000, 94.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein lsr2


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 / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.39 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 16, 2011 / Details: msc osmic optics
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.728→1.82 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 6.9 / % possible all: 96.3

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
Arcimboldophasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1852 502 4.77 %
Rwork0.16 --
obs0.1613 10528 99.43 %
Solvent computationShrinkage 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 parametersBiso max: 39.39 Å2 / Biso mean: 13.575 Å2 / Biso min: 3.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.7273 Å20 Å2-0.3355 Å2
2--1.3752 Å20 Å2
3----2.1025 Å2
Refinement stepCycle: LAST / Resolution: 1.728→29.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms834 0 0 206 1040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006842
X-RAY DIFFRACTIONf_angle_d0.9141139
X-RAY DIFFRACTIONf_chiral_restr0.063136
X-RAY DIFFRACTIONf_plane_restr0.003147
X-RAY DIFFRACTIONf_dihedral_angle_d11.561295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.728-1.90240.25281070.19512470257798
1.9024-2.17760.19171270.145224752602100
2.1776-2.74320.1761370.157525052642100
2.7432-29.10150.1731310.158425762707100

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