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- PDB-6y5u: MenT3 (aka TglT), nucleotidyltransferase toxin Rv1045 from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 6y5u
TitleMenT3 (aka TglT), nucleotidyltransferase toxin Rv1045 from Mycobacterium tuberculosis
ComponentsRv1045
KeywordsTOXIN / Nucleotidyltransferase Toxin-antitoxin system Mycobacterium tuberculosis
Function / homologyNucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyl transferase AbiEii toxin, Type IV TA system / metal ion binding / Nucleotidyl transferase AbiEii/AbiGii toxin family protein
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.59 Å
AuthorsBlower, T.R. / Usher, B.
CitationJournal: Sci Adv / Year: 2020
Title: A nucleotidyltransferase toxin inhibits growth of Mycobacterium tuberculosis through inactivation of tRNA acceptor stems.
Authors: Cai, Y. / Usher, B. / Gutierrez, C. / Tolcan, A. / Mansour, M. / Fineran, P.C. / Condon, C. / Neyrolles, O. / Genevaux, P. / Blower, T.R.
History
DepositionFeb 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 20, 2021Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rv1045


Theoretical massNumber of molelcules
Total (without water)31,9781
Polymers31,9781
Non-polymers00
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.410, 95.410, 69.026
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 Rv1045


Mass: 31978.451 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 (E. coli) / References: UniProt: P96356
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 56.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium Acetate Hydrate 0.1 M Tris pH 8.5 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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.59→52.97 Å / Num. obs: 49008 / % possible obs: 99.95 % / Redundancy: 2 % / Biso Wilson estimate: 26.57 Å2 / CC1/2: 1 / Net I/σ(I): 16.68
Reflection shellResolution: 1.59→1.647 Å / Num. unique obs: 4834 / CC1/2: 0.672

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.59→52.97 Å / SU ML: 0.2067 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7057
RfactorNum. reflection% reflection
Rfree0.2249 2437 4.97 %
Rwork0.2024 --
obs0.2036 49001 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.08 Å2
Refinement stepCycle: LAST / Resolution: 1.59→52.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 0 281 2494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592260
X-RAY DIFFRACTIONf_angle_d0.93683086
X-RAY DIFFRACTIONf_chiral_restr0.0529361
X-RAY DIFFRACTIONf_plane_restr0.007404
X-RAY DIFFRACTIONf_dihedral_angle_d22.1597830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.620.31361520.30742651X-RAY DIFFRACTION99.22
1.62-1.660.30261600.2692725X-RAY DIFFRACTION99.97
1.66-1.70.26871730.26372653X-RAY DIFFRACTION99.93
1.7-1.740.29971430.24372737X-RAY DIFFRACTION99.93
1.74-1.790.28761090.23582738X-RAY DIFFRACTION99.93
1.79-1.840.25041410.22152710X-RAY DIFFRACTION99.96
1.84-1.90.23121780.21722689X-RAY DIFFRACTION100
1.9-1.970.25661170.2212742X-RAY DIFFRACTION100
1.97-2.040.22881060.21352761X-RAY DIFFRACTION100
2.04-2.140.25431320.20442741X-RAY DIFFRACTION99.97
2.14-2.250.25991340.21692741X-RAY DIFFRACTION99.97
2.25-2.390.27961140.21752779X-RAY DIFFRACTION100
2.39-2.580.26451350.21562750X-RAY DIFFRACTION100
2.58-2.830.26051240.21772759X-RAY DIFFRACTION100
2.83-3.240.22271850.20432731X-RAY DIFFRACTION100
3.24-4.090.20111560.17792794X-RAY DIFFRACTION100
4.09-52.970.18271780.17732863X-RAY DIFFRACTION99.87

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