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- PDB-4e1r: Crystal structure of the dimerization domain of Lsr2 from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 4e1r
TitleCrystal structure of the dimerization domain of Lsr2 from Mycobacterium tuberculosis in the P 31 2 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 / cytosol / cytoplasm
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.041 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 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein lsr2
B: Protein lsr2


Theoretical massNumber of molelcules
Total (without water)19,2832
Polymers19,2832
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-19 kcal/mol
Surface area6780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.390, 57.390, 105.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein lsr2


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 / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 27, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.041→52.655 Å / Num. obs: 13341 / Redundancy: 20.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 22.6
Reflection shellResolution: 2.041→2.15 Å / Redundancy: 20.5 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
PHASERMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E1P

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
RfactorNum. reflection% reflection
Rfree0.2871 1323 10 %
Rwork0.251 --
obs0.2547 13232 99.44 %
Solvent computationShrinkage 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 parametersBiso max: 70.88 Å2 / Biso mean: 36.6759 Å2 / Biso min: 20.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.3257 Å2-0 Å2-0 Å2
2--1.3257 Å20 Å2
3----2.6513 Å2
Refinement stepCycle: LAST / Resolution: 2.041→36.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms838 0 0 135 973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008846
X-RAY DIFFRACTIONf_angle_d0.9971143
X-RAY DIFFRACTIONf_chiral_restr0.068136
X-RAY DIFFRACTIONf_plane_restr0.003147
X-RAY DIFFRACTIONf_dihedral_angle_d14.402299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.041-2.12290.33691430.283213191462100
2.1229-2.21950.34371430.300712841427100
2.2195-2.33650.45861310.41831248137995
2.3365-2.48280.31751480.287813111459100
2.4828-2.67450.32341490.28213031452100
2.6745-2.94350.29671480.284313251473100
2.9435-3.36920.31131520.249513491501100
3.3692-4.24380.23891550.210913321487100
4.2438-36.14880.23871540.20414381592100

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