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- PDB-5mtw: Mycobacterium tuberculosis Rv1957 SecB-like chaperone in complex ... -

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Basic information

Entry
Database: PDB / ID: 5mtw
TitleMycobacterium tuberculosis Rv1957 SecB-like chaperone in complex with a ChAD peptide from Rv1956 HigA1 antitoxin
Components
  • Antitoxin HigA1
  • SecB-like chaperone Rv1957
KeywordsCHAPERONE / Toxin-antitoxin-chaperone system / Complex
Function / homology
Function and homology information


positive regulation of growth / toxin sequestering activity / negative regulation of growth / cell wall / response to hypoxia / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
SecB-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
SecB-like chaperone Rv1957 / Antitoxin HigA1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Mycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsGuillet, V. / Mourey, L.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BSV8-0010-01 France
Citation
Journal: Nat Commun / Year: 2019
Title: Structural insights into chaperone addiction of toxin-antitoxin systems.
Authors: Guillet, V. / Bordes, P. / Bon, C. / Marcoux, J. / Gervais, V. / Sala, A.J. / Dos Reis, S. / Slama, N. / Mares-Mejia, I. / Cirinesi, A.M. / Maveyraud, L. / Genevaux, P. / Mourey, L.
#1: Journal: Nat Commun / Year: 2016
Title: Chaperone addiction of toxin-antitoxin systems.
Authors: Bordes, P. / Sala, A.J. / Ayala, S. / Texier, P. / Slama, N. / Cirinesi, A.M. / Guillet, V. / Mourey, L. / Genevaux, P.
History
DepositionJan 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: SecB-like chaperone Rv1957
D: SecB-like chaperone Rv1957
A: SecB-like chaperone Rv1957
B: SecB-like chaperone Rv1957
E: Antitoxin HigA1
F: Antitoxin HigA1
G: Antitoxin HigA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,68712
Polymers86,4117
Non-polymers2775
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-81 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.860, 89.960, 91.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SecB-like chaperone Rv1957


Mass: 20409.609 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: secBL, Rv1957 / Production host: Escherichia coli (E. coli) / References: UniProt: P95257
#2: Protein/peptide Antitoxin HigA1


Mass: 1590.762 Da / Num. of mol.: 3 / Fragment: UNP Residues 104-116 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)
References: UniProt: P9WJA7
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 25-27 % PEG 1500, calcium acetate 80-240 mM, 10 % DMSO, 100 mM Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072522 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072522 Å / Relative weight: 1
ReflectionResolution: 1.835→64.09 Å / Num. obs: 63188 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.7
Reflection shellResolution: 1.835→1.867 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3135 / CC1/2: 0.338 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSautoPROC 1.1.7data reduction
XSCALEautoPROC 1.1.7data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FX3

1fx3


Resolution: 1.84→64.09 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.601 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.138
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26488 3397 5.4 %RANDOM
Rwork0.21156 ---
obs0.2144 59790 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.913 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.84→64.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4585 0 11 49 4645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194701
X-RAY DIFFRACTIONr_bond_other_d0.0010.024416
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.9696411
X-RAY DIFFRACTIONr_angle_other_deg0.906310061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7045573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58622.489229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0515694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4121550
X-RAY DIFFRACTIONr_chiral_restr0.120.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215296
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021106
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4093.2822331
X-RAY DIFFRACTIONr_mcbond_other3.413.2812330
X-RAY DIFFRACTIONr_mcangle_it4.5744.8642888
X-RAY DIFFRACTIONr_mcangle_other4.5734.8642889
X-RAY DIFFRACTIONr_scbond_it3.7433.5762370
X-RAY DIFFRACTIONr_scbond_other3.7423.5762371
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6335.2343523
X-RAY DIFFRACTIONr_long_range_B_refined7.49825.4674907
X-RAY DIFFRACTIONr_long_range_B_other7.525.4464903
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.835→1.883 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 275 -
Rwork0.33 4325 -
obs--99.89 %

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