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- PDB-5dlo: S. aureus MazF in complex with substrate analogue -

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Basic information

Entry
Database: PDB / ID: 5dlo
TitleS. aureus MazF in complex with substrate analogue
Components
  • DNA substrate analogue AUACAUA
  • Endoribonuclease MazF
KeywordsHYDROLASE / Toxin-Antitoxin / mRNA interferase / ribonuclease / persistence / bacterial stress response
Function / homology
Function and homology information


rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / 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
DNA / Endoribonuclease MazF / Endoribonuclease MazF
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Enterobacterio phage MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å
AuthorsZorzini, V. / Loris, R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds Wetenschappelijk Onderzoek Belgium
CitationJournal: To Be Published
Title: Substrate recognition, regulation mechanism and activity regulation of MazF mRNA interferase.
Authors: Zorzini, V. / Loris, R.
History
DepositionSep 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2Jan 10, 2024Group: 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
Revision 1.3Jul 24, 2024Group: Database references / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_name_com.name / _entity_src_gen.pdbx_gene_src_gene ..._entity_name_com.name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoribonuclease MazF
B: DNA substrate analogue AUACAUA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0653
Polymers17,0302
Non-polymers351
Water3,513195
1
A: Endoribonuclease MazF
B: DNA substrate analogue AUACAUA
hetero molecules

A: Endoribonuclease MazF
B: DNA substrate analogue AUACAUA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1306
Polymers34,0594
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
Buried area7060 Å2
ΔGint-24 kcal/mol
Surface area10610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.600, 63.600, 69.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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


Mass: 14952.206 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mazF, SA1873 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7A4G9, UniProt: Q2FWI8*PLUS, Hydrolases; Acting on ester bonds
#2: DNA chain DNA substrate analogue AUACAUA


Mass: 2077.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacterio phage MS2 (virus)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 75 mM Tris pH 8.5, 18.75% v/v tert-Butanol, 25% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.4→31.8 Å / Num. obs: 31425 / % possible obs: 99 % / Redundancy: 5.4 % / Rsym value: 0.048 / Net I/σ(I): 21.64
Reflection shellResolution: 1.4→1.49 Å / Mean I/σ(I) obs: 2.03 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MZM

4mzm


Resolution: 1.401→31.8 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1634 1571 5 %
Rwork0.1329 --
obs0.1344 31425 99.79 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.992 Å2 / ksol: 0.416 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0848 Å20 Å20 Å2
2---1.0848 Å2-0 Å2
3---2.1695 Å2
Refinement stepCycle: LAST / Resolution: 1.401→31.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms869 138 1 195 1203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061045
X-RAY DIFFRACTIONf_angle_d1.2531441
X-RAY DIFFRACTIONf_dihedral_angle_d13.227417
X-RAY DIFFRACTIONf_chiral_restr0.098174
X-RAY DIFFRACTIONf_plane_restr0.004160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4009-1.44610.3711410.3122665X-RAY DIFFRACTION98
1.4461-1.49780.24411420.2192702X-RAY DIFFRACTION100
1.4978-1.55780.20251410.16722704X-RAY DIFFRACTION100
1.5578-1.62870.1831440.14132726X-RAY DIFFRACTION100
1.6287-1.71460.17531420.12082706X-RAY DIFFRACTION100
1.7146-1.8220.15131420.10692701X-RAY DIFFRACTION100
1.822-1.96260.1361430.10162713X-RAY DIFFRACTION100
1.9626-2.16010.14381430.11812728X-RAY DIFFRACTION100
2.1601-2.47260.15791440.11872721X-RAY DIFFRACTION100
2.4726-3.11470.16691430.1342731X-RAY DIFFRACTION100
3.1147-31.80820.14721460.13112757X-RAY DIFFRACTION99

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