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- PDB-4ml2: Crystal structure of wild-type YafQ -

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Basic information

Entry
Database: PDB / ID: 4ml2
TitleCrystal structure of wild-type YafQ
ComponentsmRNA interferase YafQ
KeywordsTOXIN / antitoxin
Function / homology
Function and homology information


toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / translational termination / RNA endonuclease activity / ribosome binding / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / Hydrolases; Acting on ester bonds / response to antibiotic ...toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / translational termination / RNA endonuclease activity / ribosome binding / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / Hydrolases; Acting on ester bonds / response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / RNA binding
Similarity search - Function
Toxin-antitoxin system, YafQ-like toxin / Bacterial toxin of type II toxin-antitoxin system, YafQ / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
mRNA interferase toxin YafQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLiang, Y.J. / Gao, Z.Q. / Liu, Q.S. / Dong, Y.H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural and Functional Characterization of Escherichia coli Toxin-Antitoxin Complex DinJ-YafQ
Authors: Liang, Y. / Gao, Z. / Wang, F. / Zhang, Y. / Dong, Y. / Liu, Q.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRNA interferase YafQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5916
Polymers11,1111
Non-polymers4805
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.299, 89.832, 75.015
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein mRNA interferase YafQ / Endoribonuclease YafQ / Toxin YafQ


Mass: 11110.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yafQ, b0225, JW0215 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q47149, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M (NH4)2SO4, 30% PEG8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 19, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 22814 / Num. obs: 22754 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 72.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 16.3 / Num. unique all: 1104 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MMG

4mmg


Resolution: 1.5→28.79 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 15.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1892 1163 5.11 %random
Rwork0.1757 ---
all0.1764 22814 --
obs0.1757 22746 99.99 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.103 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2061 Å20 Å2-0 Å2
2---2.0502 Å20 Å2
3----0.6431 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms749 0 25 217 991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006810
X-RAY DIFFRACTIONf_angle_d1.0841098
X-RAY DIFFRACTIONf_dihedral_angle_d12.545304
X-RAY DIFFRACTIONf_chiral_restr0.076112
X-RAY DIFFRACTIONf_plane_restr0.005135
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.5-1.56830.25811310.2182644
1.5683-1.6510.21961560.18162675
1.651-1.75440.19131570.16392629
1.7544-1.88980.20031420.16382673
1.8898-2.07990.18341320.16852708
2.0799-2.38080.16481480.172696
2.3808-2.9990.19891530.17532714
2.999-28.79490.17891440.17962844

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