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- PDB-7du4: The structure of the M.tb MazF-mt9 toxin in complex with a fragme... -

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Basic information

Entry
Database: PDB / ID: 7du4
TitleThe structure of the M.tb MazF-mt9 toxin in complex with a fragment of cognate antitoxin
Components
  • Probable endoribonuclease MazF7
  • peptide
KeywordsTOXIN / Mycobacterium tuberculosis / anti-bacterial peptide
Function / homology
Function and homology information


modulation by symbiont of host process / negative regulation of growth / rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / negative regulation of translation / Hydrolases; Acting on ester bonds / DNA binding
Similarity search - Function
mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor
Similarity search - Domain/homology
Probable endoribonuclease MazF7
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsXie, W. / Chen, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870782 China
CitationJournal: Toxins / Year: 2021
Title: Mechanistic Insight into the Peptide Binding Modes to Two M. tb MazF Toxins.
Authors: Chen, R. / Zhou, J. / Xie, W.
History
DepositionJan 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable endoribonuclease MazF7
B: Probable endoribonuclease MazF7
Q: peptide


Theoretical massNumber of molelcules
Total (without water)30,9033
Polymers30,9033
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-16 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.610, 74.610, 104.354
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: LEU / End label comp-ID: LEU

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAchain 'A'AA2 - 146 - 18
12GLYGLYchain 'A'AA23 - 11327 - 117
23ALAALA(chain 'B' and (resid 2 through 23 or (resid 24...BB2 - 146 - 18
24GLYGLY(chain 'B' and (resid 2 through 23 or (resid 24...BB23 - 11327 - 117

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Components

#1: Protein Probable endoribonuclease MazF7 / Toxin MazF7


Mass: 14633.806 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: mazF7, Rv2063A / Production host: Escherichia coli (E. coli)
References: UniProt: P0CL62, Hydrolases; Acting on ester bonds
#2: Protein/peptide peptide /


Mass: 1635.623 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1.5 M NaCl,0.1 M NaOAc pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 17270 / % possible obs: 100 % / Redundancy: 19.2 % / Biso Wilson estimate: 27.66 Å2 / CC1/2: 0.935 / Rmerge(I) obs: 0.205 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 4.15 / Num. unique obs: 1730 / CC1/2: 0.945

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A6X

6a6x


Resolution: 2.18→37.31 Å / SU ML: 0.2574 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 22.4736 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.225 852 5.13 %
Rwork0.1829 15747 -
obs0.185 16599 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.49 Å2
Refinement stepCycle: LAST / Resolution: 2.18→37.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 0 117 1749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661653
X-RAY DIFFRACTIONf_angle_d0.98672253
X-RAY DIFFRACTIONf_chiral_restr0.0579282
X-RAY DIFFRACTIONf_plane_restr0.0071291
X-RAY DIFFRACTIONf_dihedral_angle_d2.95231025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.320.2521240.20672168X-RAY DIFFRACTION80.17
2.32-2.50.25331580.21152701X-RAY DIFFRACTION99.55
2.5-2.750.25351590.2012694X-RAY DIFFRACTION99.93
2.75-3.140.26721330.19092723X-RAY DIFFRACTION99.93
3.14-3.960.18241610.16682711X-RAY DIFFRACTION99.97
3.96-37.310.21871170.17212750X-RAY DIFFRACTION98.79

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