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- PDB-8rr6: MenT3 (aka TglT) toxin (Rv1045) from Mycobacterium tuberculosis H... -

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Basic information

Entry
Database: PDB / ID: 8rr6
TitleMenT3 (aka TglT) toxin (Rv1045) from Mycobacterium tuberculosis H37Rv, non-phosphorylated
ComponentsNucleotidyl transferase AbiEii/AbiGii toxin family protein
KeywordsTOXIN / Nucleotidyltransferase / phosphorylation / translation
Function / homologyNucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyl transferase AbiEii toxin, Type IV TA system / nucleotide binding / metal ion binding / Nucleotidyl transferase AbiEii/AbiGii toxin family protein
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsArrowsmith, T.J. / Blower, T.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/S022791/1 United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: Inducible auto-phosphorylation regulates a widespread family of nucleotidyltransferase toxins.
Authors: Arrowsmith, T.J. / Xu, X. / Xu, S. / Usher, B. / Stokes, P. / Guest, M. / Bronowska, A.K. / Genevaux, P. / Blower, T.R.
History
DepositionJan 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleotidyl transferase AbiEii/AbiGii toxin family protein


Theoretical massNumber of molelcules
Total (without water)31,8981
Polymers31,8981
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13520 Å2
Unit cell
Length a, b, c (Å)95.272, 95.272, 69.028
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Nucleotidyl transferase AbiEii/AbiGii toxin family protein


Mass: 31898.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: Rv1045 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P96356
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.84 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M calcium acetate hydrate, 0.1 M Tris pH 8.5 and 25% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→41.25 Å / Num. obs: 34876 / % possible obs: 97.35 % / Redundancy: 19.9 % / Biso Wilson estimate: 44.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09663 / Rrim(I) all: 0.09921 / Net I/σ(I): 12.64
Reflection shellResolution: 1.78→1.845 Å / Redundancy: 20 % / Rmerge(I) obs: 5.678 / Mean I/σ(I) obs: 0.27 / Num. unique obs: 3443 / CC1/2: 0.587 / Rrim(I) all: 5.822 / % possible all: 75.14

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Processing

Software
NameVersionClassification
REFMAC1.18.2_3874refinement
PHENIX1.18.2_3874refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→41.25 Å / SU ML: 0.3212 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.7575
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2229 1741 5.12 %
Rwork0.2066 32268 -
obs0.2074 34009 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.28 Å2
Refinement stepCycle: LAST / Resolution: 1.78→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2209 0 0 79 2288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01092256
X-RAY DIFFRACTIONf_angle_d1.45853079
X-RAY DIFFRACTIONf_chiral_restr0.2818361
X-RAY DIFFRACTIONf_plane_restr0.0102404
X-RAY DIFFRACTIONf_dihedral_angle_d22.5575828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.830.44831300.41721900X-RAY DIFFRACTION70.41
1.83-1.890.40211450.38082706X-RAY DIFFRACTION99.13
1.89-1.960.30471670.32882707X-RAY DIFFRACTION99.62
1.96-2.040.28571290.26712731X-RAY DIFFRACTION99.58
2.04-2.130.27831480.23472732X-RAY DIFFRACTION99.83
2.13-2.240.25121650.20472712X-RAY DIFFRACTION99.86
2.24-2.390.23271580.21572752X-RAY DIFFRACTION99.93
2.39-2.570.22031320.19822760X-RAY DIFFRACTION99.97
2.57-2.830.22711200.232776X-RAY DIFFRACTION100
2.83-3.240.24991390.21972790X-RAY DIFFRACTION100
3.24-4.080.18941610.19542796X-RAY DIFFRACTION100
4.08-41.250.20661470.18052906X-RAY DIFFRACTION99.93

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