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- PDB-4mzt: MazF from S. aureus crystal form II, C2221, 2.3 A -

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Basic information

Entry
Database: PDB / ID: 4mzt
TitleMazF from S. aureus crystal form II, C2221, 2.3 A
ComponentsMazF mRNA interferase
KeywordsHYDROLASE / CcdB/MazF fold / ribonuclease / MazE
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: 2.303 Å
AuthorsZorzini, V. / Loris, R. / van Nuland, N.A.J. / Cheung, A.
Citation
Journal: Nucleic Acids Res. / Year: 2014
Title: Structural and biophysical characterization of Staphylococcus aureus SaMazF shows conservation of functional dynamics.
Authors: Zorzini, V. / Buts, L. / Sleutel, M. / Garcia-Pino, A. / Talavera, A. / Haesaerts, S. / Greve, H.D. / Cheung, A. / van Nuland, N.A. / Loris, R.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization of the Staphylococcus aureus MazF mRNA interferase.
Authors: Zorzini, V. / Haesaerts, S. / Donegan, N.P. / Fu, Z. / Cheung, A.L. / van Nuland, N.A. / Loris, R.
#2: Journal: Biomol.Nmr Assign. / Year: 2011
Title: 1H, 13C, and 15N backbone and side-chain chemical shift assignment of the staphylococcal MazF mRNA interferase.
Authors: Zorzini, V. / Haesaerts, S. / Cheung, A. / Loris, R. / van Nuland, N.A.
History
DepositionSep 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Sep 20, 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 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,9042
Polymers29,9042
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-9 kcal/mol
Surface area10180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.588, 92.007, 71.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:113 )
211chain B and (resseq 1:113 )

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Components

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


Mass: 14952.206 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: N315 / Gene: mazF, SA1873 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7A4G9, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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 Å3/Da / Density % sol: 38.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Na-HEPES pH 7.5, 2.0 M NH4HCO2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0394 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0394 Å / Relative weight: 1
ReflectionResolution: 2.3→46 Å / Num. all: 10915 / Num. obs: 10915 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 11.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4(Phaser)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4(Phaser)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MZM

4mzm


Resolution: 2.303→46 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 521 4.8 %random
Rwork0.1955 ---
obs0.198 10859 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.109 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.5977 Å2-0 Å2-0 Å2
2---4.3676 Å20 Å2
3----4.2302 Å2
Refinement stepCycle: LAST / Resolution: 2.303→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 0 67 1743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091694
X-RAY DIFFRACTIONf_angle_d1.2912302
X-RAY DIFFRACTIONf_dihedral_angle_d12.841627
X-RAY DIFFRACTIONf_chiral_restr0.091288
X-RAY DIFFRACTIONf_plane_restr0.006294
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A820X-RAY DIFFRACTIONPOSITIONAL
12B820X-RAY DIFFRACTIONPOSITIONAL0.064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.303-2.53430.31911330.222528X-RAY DIFFRACTION99
2.5343-2.90090.33271210.24432557X-RAY DIFFRACTION99
2.9009-3.65460.25381290.19752591X-RAY DIFFRACTION100
3.6546-46.01270.19271380.17042662X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.58660.6190.00062.36510.46511.76250.0312-0.04370.01430.10560.0578-0.0619-0.1510.0364-0.09830.1406-0.01610.02490.106-0.00640.1128-10.292417.9187-0.8005
22.00920.47330.3731.5975-0.04421.63050.03240.20540.0049-0.14210.07780.03570.0621-0.1509-0.1190.0888-0.02120.00430.13120.03080.0903-17.98029.9011-17.5048
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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