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- PDB-5wyg: The crystal structure of the apo form of Mtb MazF -

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Basic information

Entry
Database: PDB / ID: 5wyg
TitleThe crystal structure of the apo form of Mtb MazF
ComponentsProbable endoribonuclease MazF7
KeywordsHYDROLASE / Mycobacterium tuberculosis / Toxin-antitoxin system / MazF
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 / negative regulation of translation / 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
Probable endoribonuclease MazF7
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.356 Å
AuthorsXie, W. / Chen, R. / Tu, J.
Funding support China, 3items
OrganizationGrant numberCountry
the Science and Technology Program of Guangzhou201504010025 China
the Fundamental Research Funds for the Central Universities16lgjc76 China
Guangdong Innovative Research Team ProgramNO. 2011Y038 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structure of the MazF-mt9 toxin, a tRNA-specific endonuclease from Mycobacterium tuberculosis
Authors: Chen, R. / Tu, J. / Liu, Z. / Meng, F. / Ma, P. / Ding, Z. / Yang, C. / Chen, L. / Deng, X. / Xie, W.
History
DepositionJan 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable endoribonuclease MazF7
C: Probable endoribonuclease MazF7


Theoretical massNumber of molelcules
Total (without water)29,3042
Polymers29,3042
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-13 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.468, 74.468, 105.114
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Probable endoribonuclease MazF7 / Toxin MazF7


Mass: 14651.845 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: mazF7, Rv2063A / Production host: Escherichia coli (E. coli)
References: UniProt: P0CL62, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 1.5 M NaCl, 0.1 M NaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 13737 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 18.5
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 1364 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CKF

5ckf


Resolution: 2.356→37.234 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 677 4.95 %
Rwork0.1896 --
obs0.1914 13668 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.356→37.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 0 56 1608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061572
X-RAY DIFFRACTIONf_angle_d1.0022144
X-RAY DIFFRACTIONf_dihedral_angle_d17.52988
X-RAY DIFFRACTIONf_chiral_restr0.063273
X-RAY DIFFRACTIONf_plane_restr0.008275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.356-2.53790.29061480.23322568X-RAY DIFFRACTION99
2.5379-2.79320.23921400.21442590X-RAY DIFFRACTION100
2.7932-3.19720.23951260.20882601X-RAY DIFFRACTION100
3.1972-4.02740.23961420.18582591X-RAY DIFFRACTION100
4.0274-37.23860.18411210.16892641X-RAY DIFFRACTION100

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