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- PDB-8ypj: Cyrstal structure of the MazE-mt10 Antitoxin from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 8ypj
TitleCyrstal structure of the MazE-mt10 Antitoxin from Mycobacterium tuberculosis
ComponentsAntitoxin
KeywordsSIGNALING PROTEIN / Antitoxin / MazE / Mycobacterium tuberculosis / DNA binding
Function / homologyRibbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / regulation of DNA-templated transcription / DNA binding / PHOSPHATE ION / Antitoxin
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsLee, K.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-RS-2022-00166782 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: DNA binding reveals hidden interdomain allostery of a MazE antitoxin from Mycobacterium tuberculosis.
Authors: Eun, H.J. / Lee, S.Y. / Lee, K.Y.
History
DepositionMar 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antitoxin
B: Antitoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3773
Polymers16,2822
Non-polymers951
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-27 kcal/mol
Surface area6270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.370, 99.370, 99.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Antitoxin / CopG family DNA-binding protein / Ribbon-helix-helix protein / CopG family


Mass: 8141.198 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A045H4M5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES (pH 6), 20% (w/v) PEG 6000, 0.2 M NH4Cl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97959 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 1.91→30 Å / Num. obs: 12759 / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 21.3
Reflection shellResolution: 1.91→1.94 Å / Rmerge(I) obs: 0.097 / Num. unique obs: 648

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000712data reduction
HKL-2000712data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: SAD / Resolution: 1.91→30 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 630 4.87 %
Rwork0.2002 --
obs0.2022 12759 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms763 0 5 44 812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007769
X-RAY DIFFRACTIONf_angle_d0.881037
X-RAY DIFFRACTIONf_dihedral_angle_d12.724287
X-RAY DIFFRACTIONf_chiral_restr0.037128
X-RAY DIFFRACTIONf_plane_restr0.003134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-2.10.27341470.24213050X-RAY DIFFRACTION100
2.1-2.40.24931700.19513033X-RAY DIFFRACTION100
2.4-3.020.24311600.1983058X-RAY DIFFRACTION100

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