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- PDB-8rr5: MenT1 toxin (rv0078a) from Mycobacterium tuberculosis H37Rv, phos... -

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Basic information

Entry
Database: PDB / ID: 8rr5
TitleMenT1 toxin (rv0078a) from Mycobacterium tuberculosis H37Rv, phosphorylated at T39
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 / Nucleotidyltransferase superfamily / Nucleotidyl transferase AbiEii/AbiGii toxin family protein
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)21,5891
Polymers21,5891
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Evidence of phosphorylated structure in vivo in Mtb.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.001, 127.001, 68.776
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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


Mass: 21589.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: Rv0078A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L7N686
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.59 Å3/Da / Density % sol: 65.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 4 M Sodium Formate, 0.1 M Tris, pH 7.5 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 17, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→63.58 Å / Num. obs: 7213 / % possible obs: 100 % / Redundancy: 1.8 % / Biso Wilson estimate: 71.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.014 / Rrim(I) all: 0.02 / Net I/σ(I): 27.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1035 / CC1/2: 0.992 / Rrim(I) all: 0.105 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→63.58 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 16.373 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 0.55 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23939 361 5 %RANDOM
Rwork0.19683 ---
obs0.19906 6853 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.14 Å2
Baniso -1Baniso -2Baniso -3
1--6.75 Å20 Å20 Å2
2---6.75 Å20 Å2
3---13.49 Å2
Refinement stepCycle: 1 / Resolution: 2.8→63.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1357 0 0 3 1360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121371
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161374
X-RAY DIFFRACTIONr_angle_refined_deg1.481.6341862
X-RAY DIFFRACTIONr_angle_other_deg0.4811.5693126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4735173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.664518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53110233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02318
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_it5.7137.134701
X-RAY DIFFRACTIONr_mcbond_other5.6497.139701
X-RAY DIFFRACTIONr_mcangle_it8.49212.773871
X-RAY DIFFRACTIONr_mcangle_other8.52312.78872
X-RAY DIFFRACTIONr_scbond_it7.3368.175670
X-RAY DIFFRACTIONr_scbond_other7.3338.181671
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.22314.605992
X-RAY DIFFRACTIONr_long_range_B_refined14.30967.791493
X-RAY DIFFRACTIONr_long_range_B_other14.30467.821494
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 21 -
Rwork0.373 501 -
obs--100 %

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