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- PDB-7du5: The structure of the M.tb MazF-mt1 toxin in complex with a fragme... -

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Basic information

Entry
Database: PDB / ID: 7du5
TitleThe structure of the M.tb MazF-mt1 toxin in complex with a fragment of cognate antitoxin
Components
  • A fragment of MazE-mt1
  • Endoribonuclease MazF9
KeywordsTOXIN / Mycobacterium tuberculosis / MazF / cocrystal structure / antibacterial peptide
Function / homology
Function and homology information


symbiont-mediated perturbation of host process / negative regulation of growth / rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / 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
Endoribonuclease MazF9
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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: Endoribonuclease MazF9
B: Endoribonuclease MazF9
C: A fragment of MazE-mt1


Theoretical massNumber of molelcules
Total (without water)28,4673
Polymers28,4673
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-14 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.271, 83.271, 141.265
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
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,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 2 - 116 / Label seq-ID: 6 - 120

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and (resid 2 through 68 or (resid 69...AA
22(chain 'B' and (resid 2 or (resid 3 and (name...BB

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Components

#1: Protein Endoribonuclease MazF9 / Toxin MazF9 / mRNA interferase MazF-mt1


Mass: 13270.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: mazF9, mazF-mt1, Rv2801c / Production host: Escherichia coli (E. coli)
References: UniProt: P71650, Hydrolases; Acting on ester bonds
#2: Protein/peptide A fragment of MazE-mt1


Mass: 1926.946 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)

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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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG 3350, 0.1 M NaOAc pH 5.0, 0.1 M NaCl

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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 6M / Detector: PIXEL / Date: Dec 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.65→41.64 Å / Num. obs: 8929 / % possible obs: 99.8 % / Redundancy: 18.8 % / Biso Wilson estimate: 67.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.5
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 20.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 1158 / CC1/2: 0.99 / % possible all: 99.6

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Processing

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

6kyt


Resolution: 2.65→41.64 Å / SU ML: 0.3724 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.7292 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2804 421 4.73 %
Rwork0.2542 8488 -
obs0.2554 8909 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.92 Å2
Refinement stepCycle: LAST / Resolution: 2.65→41.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 0 0 1873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621899
X-RAY DIFFRACTIONf_angle_d1.09622594
X-RAY DIFFRACTIONf_chiral_restr0.0579313
X-RAY DIFFRACTIONf_plane_restr0.0075341
X-RAY DIFFRACTIONf_dihedral_angle_d8.27921155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-3.030.30531360.31682731X-RAY DIFFRACTION99.2
3.03-3.820.30771520.29562776X-RAY DIFFRACTION99.73
3.82-41.640.26251330.22752981X-RAY DIFFRACTION99.71
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.418987775441.72012336701-3.363020778275.20085696128-1.838760241622.0410469517-0.08052691998711.38834279689-0.595171154011-1.2262106726-0.133352600893-0.2061363889930.207110492329-0.5686114174110.2171956713890.4976271361010.00286628725305-0.08463019740181.26237834857-0.1077066052590.62730575071826.436302508896.13791328320.912222372251
24.79734072556-1.32501643965-2.509762745964.28577398518-0.9107566563546.17208074267-0.2553342978982.70100344730.213817701129-0.8090907827910.44628365333-0.126375882365-0.1324430883450.09507383075920.1839187678420.539036384302-0.163016028685-0.0372703877361.497295914610.2611987145050.60565054449121.2116608313101.1861653420.306917177643
35.60158733588-1.83217019172-2.354692859933.206319740770.4231882466783.50660942470.1880061239120.05632872870970.443379252227-0.0748484775825-0.296820062389-0.508400644291-0.04047629550070.787795036460.1022944360460.513364630149-0.1785558856470.04886006291661.141298034690.08894724063740.63197751085730.5718596451105.069684846.71892260777
45.057144788030.514596412041-1.45390805413.7649221481.391578813824.34965474543-0.308789333762-0.591571660178-0.121271827010.426111921257-0.220228275944-0.4023668513061.112801314980.3778277341090.317647138980.366817863618-0.119162371544-0.09141902976571.088640863060.140416668880.64111394007724.982069467599.756838374812.1888055391
56.71426368875-1.10258262121-0.6495755564954.834540399350.9757080983774.742062054320.09201394194181.621606875181.12875206543-0.4499424916320.272839376657-0.123370981548-0.3139107910650.0479825073267-0.2485958183590.5868890995410.0153733441832-0.07238687866340.9592259776240.1812019904970.73767088717910.3727603355112.1168195821.73635943434
64.213609260941.192096754551.543851730843.51661490821.430870098063.08569683594-0.6267231549030.01288646035370.432710274641-0.3996179287470.2687030127690.470619406692-0.6116952888470.05514651115220.006560972462480.523210048955-0.104869042463-0.0560331962470.9491584392660.1034614798450.70070184253814.4041294454115.65075675410.1958739253
75.50969839936-0.2882583334490.1811686676711.567194387072.003821568516.82601030099-0.9956368147991.543905073750.0610716777175-0.7170020920660.2753308339081.16772967526-0.0508608824996-1.507016204980.8621057482910.687177741022-0.233273818719-0.1375896555111.3734742261-0.03226013891560.8520385968351.6209860805198.4687768352.96658928163
82.4723168393-1.026856861783.230502242372.30250987732-2.024760366344.19753792354-0.2433779668771.02114539551.394580577960.3882427580560.3509496021230.2597301912150.14079612257-1.851658311660.0470279897840.3513530193820.0509317263651-0.121561896351.192802326430.09586782910280.9536443748970.326398378334105.9317048446.37277583716
94.95754615032-0.786248745541-2.084237172595.80642967583-1.313628173923.07813131426-0.1183613392090.9215882388541.59088591805-0.2479806605550.04222971458230.0895302919965-0.596976042376-0.1941552240750.03576120598910.693638113211-0.00934702057532-0.1856613662541.010412254790.2166021416570.92341749499110.4588523652115.4162618855.27830241241
102.16660794658-5.60716386762-5.261047237232.231022991595.010932087655.91204753695-0.48022030133-0.047075502966-1.820608788140.871234800362-0.3517125550071.329288179020.666793315117-0.3176361451040.6663124314310.427601064037-0.1752339397260.002557703118230.803833221512-0.01187871828090.7393051197610.114542785699.40800268915.1268908108
114.480507484670.191378503745-0.8538297960122.53729358761-1.755615228741.858386856840.780898783922-0.2027774956161.454476672030.5167595624230.244047732001-0.855589585187-1.74883239183-0.113613224818-1.174477454050.860800979294-0.5265902510850.1576193823651.180486769530.163386635241.0263129443828.4580303247117.44008874812.1608956034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 11 )
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 118 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 22 )
6X-RAY DIFFRACTION6chain 'B' and (resid 23 through 50 )
7X-RAY DIFFRACTION7chain 'B' and (resid 51 through 61 )
8X-RAY DIFFRACTION8chain 'B' and (resid 62 through 82 )
9X-RAY DIFFRACTION9chain 'B' and (resid 83 through 99 )
10X-RAY DIFFRACTION10chain 'B' and (resid 100 through 117 )
11X-RAY DIFFRACTION11chain 'C' and (resid 42 through 56 )

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