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- PDB-7ewi: Toxin protein from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 7ewi
TitleToxin protein from Staphylococcus aureus
ComponentsEndoribonuclease MazF
KeywordsTOXIN / hydrolase RNase
Function / homologymRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / DNA binding / PHOSPHATE ION / Endoribonuclease MazF
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsKim, D.H. / Kang, S.M. / Lee, S.J. / Lee, B.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Role of PemI in the Staphylococcus aureus PemIK toxin-antitoxin complex: PemI controls PemK by acting as a PemK loop mimic.
Authors: Kim, D.H. / Kang, S.M. / Baek, S.M. / Yoon, H.J. / Jang, D.M. / Kim, H.S. / Lee, S.J. / Lee, B.J.
History
DepositionMay 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Endoribonuclease MazF
B: Endoribonuclease MazF
A: Endoribonuclease MazF
D: Endoribonuclease MazF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3119
Polymers53,8394
Non-polymers4725
Water6,684371
1
C: Endoribonuclease MazF
A: Endoribonuclease MazF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2015
Polymers26,9192
Non-polymers2823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-28 kcal/mol
Surface area10970 Å2
MethodPISA
2
B: Endoribonuclease MazF
D: Endoribonuclease MazF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1094
Polymers26,9192
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-30 kcal/mol
Surface area10610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.248, 61.422, 75.508
Angle α, β, γ (deg.)90.00, 101.20, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 13459.659 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SACH_a18 / Production host: Escherichia coli (E. coli) / References: UniProt: L7PFJ6
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 1000, 0.1 M potassium phosphate monobasic/sodium phosphate dibasic, pH 6.2, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→40 Å / Num. obs: 37045 / % possible obs: 97.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 37.9 Å2 / CC1/2: 0.988 / Net I/σ(I): 24.13
Reflection shellResolution: 1.94→1.97 Å / Num. unique obs: 1462 / CC1/2: 0.877 / % possible all: 79.8

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M1F

1m1f


Resolution: 1.93→33.95 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 1848 4.99 %
Rwork0.2026 --
obs0.2045 37010 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→33.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 26 371 4036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093717
X-RAY DIFFRACTIONf_angle_d1.2375028
X-RAY DIFFRACTIONf_dihedral_angle_d19.161493
X-RAY DIFFRACTIONf_chiral_restr0.073587
X-RAY DIFFRACTIONf_plane_restr0.008631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.32781070.25012030X-RAY DIFFRACTION73
1.98-2.040.29591390.2272651X-RAY DIFFRACTION96
2.04-2.10.23051450.20732759X-RAY DIFFRACTION99
2.1-2.180.26221450.21012751X-RAY DIFFRACTION98
2.18-2.270.27461430.20392743X-RAY DIFFRACTION99
2.27-2.370.25651460.20712759X-RAY DIFFRACTION98
2.37-2.490.21711430.21162736X-RAY DIFFRACTION99
2.49-2.650.29361450.20962752X-RAY DIFFRACTION99
2.65-2.850.2451460.22362783X-RAY DIFFRACTION99
2.85-3.140.28091460.21312769X-RAY DIFFRACTION99
3.14-3.60.20711460.19222769X-RAY DIFFRACTION99
3.6-4.530.19661460.17642786X-RAY DIFFRACTION99
4.53-33.950.2331510.2012874X-RAY DIFFRACTION99

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