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- PDB-4mzp: MazF from S. aureus crystal form III, C2221, 2.7 A -

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Basic information

Entry
Database: PDB / ID: 4mzp
TitleMazF from S. aureus crystal form III, C2221, 2.7 A
ComponentsMazF mRNA interferase
KeywordsHYDROLASE / CcdB/MazF fold / ribonuclease / MazE / mRNA interferase
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: 2.702 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

Downloads & links

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Assembly

Deposited unit
A: MazF mRNA interferase
B: MazF mRNA interferase
C: MazF mRNA interferase
D: MazF mRNA interferase
E: MazF mRNA interferase
F: MazF mRNA interferase
G: MazF mRNA interferase
H: MazF mRNA interferase


Theoretical massNumber of molelcules
Total (without water)119,6188
Polymers119,6188
Non-polymers00
Water00
1
A: MazF mRNA interferase
B: MazF mRNA interferase


Theoretical massNumber of molelcules
Total (without water)29,9042
Polymers29,9042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-9 kcal/mol
Surface area10420 Å2
MethodPISA
2
C: MazF mRNA interferase
D: MazF mRNA interferase


Theoretical massNumber of molelcules
Total (without water)29,9042
Polymers29,9042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-8 kcal/mol
Surface area10520 Å2
MethodPISA
3
E: MazF mRNA interferase
F: MazF mRNA interferase


Theoretical massNumber of molelcules
Total (without water)29,9042
Polymers29,9042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-8 kcal/mol
Surface area10320 Å2
MethodPISA
4
G: MazF mRNA interferase
H: MazF mRNA interferase


Theoretical massNumber of molelcules
Total (without water)29,9042
Polymers29,9042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-8 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.881, 92.636, 222.376
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
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:62 or resseq 70:113 )
211chain B and (resseq 1:62 or resseq 70:113 )
311chain C and (resseq 1:62 or resseq 70:113 )
411chain D and (resseq 1:62 or resseq 70:113 )
511chain E and (resseq 1:62 or resseq 70:113 )
611chain F and (resseq 1:62 or resseq 70:113 )
711chain G and (resseq 1:62 or resseq 70:113 )
811chain H and (resseq 1:62 or resseq 70:113 )

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Components

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


Mass: 14952.206 Da / Num. of mol.: 8
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

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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: 1.96 Å3/Da / Density % sol: 37.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0 M (NH4)2SO4, 0.1 M NAAC pH 4.6, 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: Feb 10, 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: 2.7→39.2 Å / Num. all: 25526 / Num. obs: 25526 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 13.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4(Phaser)model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4(Phaser)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MZM

4mzm


Resolution: 2.702→39.2 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 1251 5.08 %random
Rwork0.2085 ---
obs0.2103 24650 94.42 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.18 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4327 Å20 Å2-0 Å2
2--5.7183 Å20 Å2
3----7.151 Å2
Refinement stepCycle: LAST / Resolution: 2.702→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6707 0 0 0 6707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147003
X-RAY DIFFRACTIONf_angle_d1.3289220
X-RAY DIFFRACTIONf_dihedral_angle_d14.2112514
X-RAY DIFFRACTIONf_chiral_restr0.0931153
X-RAY DIFFRACTIONf_plane_restr0.0071181
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A781X-RAY DIFFRACTIONPOSITIONAL
12B781X-RAY DIFFRACTIONPOSITIONAL0.068
13C778X-RAY DIFFRACTIONPOSITIONAL0.061
14D768X-RAY DIFFRACTIONPOSITIONAL0.07
15E782X-RAY DIFFRACTIONPOSITIONAL0.094
16F770X-RAY DIFFRACTIONPOSITIONAL0.051
17G779X-RAY DIFFRACTIONPOSITIONAL0.054
18H793X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7025-2.81060.32591050.27352285X-RAY DIFFRACTION84
2.8106-2.93850.31811440.2452485X-RAY DIFFRACTION92
2.9385-3.09340.27281510.23412528X-RAY DIFFRACTION93
3.0934-3.28710.31631450.23172546X-RAY DIFFRACTION95
3.2871-3.54080.24281400.21052620X-RAY DIFFRACTION96
3.5408-3.89680.22791420.19142655X-RAY DIFFRACTION96
3.8968-4.460.20031410.16812699X-RAY DIFFRACTION98
4.46-5.61650.20161510.1832720X-RAY DIFFRACTION98
5.6165-39.28420.24271320.23092861X-RAY DIFFRACTION98
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)
10.78610.0560.41220.60350.07951.1063-0.0026-0.12230.05330.02190.0198-0.13-0.13220.3708-0.00490.1574-0.0012-0.03770.1686-0.03150.1342-36.51772.807232.1085
20.85580.5654-0.00160.74740.22290.90750.0118-0.0282-0.0679-0.08750.01230.02990.11430.00850.00710.14750.0065-0.01230.0604-0.01060.1226-48.0891-10.065921.8814
30.9390.28020.51190.8519-0.02241.04420.0093-0.01890.0177-0.1341-0.08310.27350.1649-0.1733-0.09830.10870.0419-0.04450.1432-0.02470.1887-55.384319.00097.3381
40.9221-0.0626-0.74981.23830.59750.79320.00450.12550.0755-0.30180.1788-0.1957-0.11470.17670.03970.1354-0.05740.02970.1445-0.02120.1644-36.360825.5597.433
51.17940.0235-0.13751-0.88511.4059-0.0355-0.01960.2485-0.12160.0995-0.0006-0.2846-0.04220.02210.1711-0.0114-0.00680.0497-0.00890.1798-44.030953.335124.6985
61.1962-0.0743-0.42540.56240.54080.94590.1179-0.2206-0.00560.2983-0.1680.26430.2139-0.4292-0.00530.1416-0.07410.06080.1911-0.02130.1619-54.958739.802333.4907
70.4233-0.4026-0.17160.99930.26170.5921-0.1295-0.6150.37060.16740.3929-0.2178-0.12670.08090.06690.17120.055-0.03860.3702-0.31840.2655-19.873452.822448.7273
80.4442-0.3388-0.08880.3973-0.10180.2129-0.2029-0.6667-0.37870.19490.31930.2379-0.0128-0.10360.19240.13440.1831-0.16490.15710.4196-0.1842-25.26933.307146.8429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

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