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- PDB-4of1: crystal structure of toxin from staphylococcus aureus Mu50 -

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Basic information

Entry
Database: PDB / ID: 4of1
Titlecrystal structure of toxin from staphylococcus aureus Mu50
ComponentsmRNA interferase MazF
KeywordsTOXIN / RNase
Function / homology
Function and homology information


rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding
Similarity search - Function
SH3 type barrels. - #110 / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Endoribonuclease MazF
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsPark, J.Y. / Im, H. / Seok, S.H. / Lee, B.J.
CitationJournal: To be Published
Title: Structural Insights into the toxin from Staphylococcus aureus Mu50
Authors: Park, J.Y. / Im, H. / Seok, S.H. / Lee, B.J.
History
DepositionJan 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA interferase MazF
B: mRNA interferase MazF


Theoretical massNumber of molelcules
Total (without water)29,0722
Polymers29,0722
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-11 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.274, 127.274, 41.916
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 14535.858 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / Gene: mazF, SAV2068 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3)
References: UniProt: Q7A2N3, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% w/v PEG 3350, 0.1 M Tris and 0.25 M lithium sulfate monohydrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2012
RadiationMonochromator: DCM Si(111)crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.45→110.22 Å / Num. obs: 14620 / Redundancy: 15.5 %
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 16.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 0.189 / Num. unique all: 1441 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→110.22 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.134 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22534 734 5 %RANDOM
Rwork0.16407 ---
obs0.16693 13872 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.428 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å2-0 Å2
2--0.17 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.45→110.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 0 77 1873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191812
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1032.0062437
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.535228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.89125.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.01615377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9521512
X-RAY DIFFRACTIONr_chiral_restr0.1290.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211272
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.447→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 55 -
Rwork0.199 937 -
obs--99.8 %

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