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- PDB-4mzm: MazF from S. aureus crystal form I, P212121, 2.1 A -

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Basic information

Entry
Database: PDB / ID: 4mzm
TitleMazF from S. aureus crystal form I, P212121, 2.1 A
ComponentsmRNA interferase MazF
KeywordsHYDROLASE / CcdB/MazF fold / ribonuclease / MazE / mRNA interferase
Function / homology
Function and homology information


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: 2.1 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 28, 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: mRNA interferase MazF
B: mRNA interferase MazF
C: mRNA interferase MazF
D: mRNA interferase MazF


Theoretical massNumber of molelcules
Total (without water)59,8094
Polymers59,8094
Non-polymers00
Water3,927218
1
A: mRNA interferase MazF
B: mRNA interferase MazF


Theoretical massNumber of molelcules
Total (without water)29,9042
Polymers29,9042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-9 kcal/mol
Surface area10480 Å2
MethodPISA
2
C: mRNA interferase MazF
D: mRNA interferase MazF


Theoretical massNumber of molelcules
Total (without water)29,9042
Polymers29,9042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-10 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.692, 65.190, 112.011
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14952.206 Da / Num. of mol.: 4
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 / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 1.85 Å3/Da / Density % sol: 33.6 %
Crystal growTemperature: 293 K / pH: 4.6
Details: 0.2 M NH4Ac, 0.1 M NaAc pH 4.6, 30% (w/v) PEG 4000, 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
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2010
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: 2.1→56.34 Å / Num. obs: 26598 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 14

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4(Phaser)model building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4(PHASER)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NE8

1ne8


Resolution: 2.1→42.48 Å / SU ML: 0.25 / σ(F): 0.11 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 1295 5.04 %
Rwork0.175 --
obs0.177 25686 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.75 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6633 Å2-0 Å20 Å2
2---5.2204 Å2-0 Å2
3---2.5571 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3387 0 0 218 3605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073431
X-RAY DIFFRACTIONf_angle_d1.0884647
X-RAY DIFFRACTIONf_dihedral_angle_d13.1721312
X-RAY DIFFRACTIONf_chiral_restr0.072572
X-RAY DIFFRACTIONf_plane_restr0.004594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18390.23691200.16512485X-RAY DIFFRACTION90
2.1839-2.28330.24221570.17572566X-RAY DIFFRACTION94
2.2833-2.40370.2711300.1782662X-RAY DIFFRACTION95
2.4037-2.55420.25881400.18712679X-RAY DIFFRACTION96
2.5542-2.75140.26181360.19662708X-RAY DIFFRACTION97
2.7514-3.02820.2581410.19052732X-RAY DIFFRACTION98
3.0282-3.46620.26271590.18792765X-RAY DIFFRACTION99
3.4662-4.36640.17821570.15212843X-RAY DIFFRACTION99
4.3664-42.48990.19611550.15632951X-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)
11.0643-0.46160.8180.454-0.57950.7501-0.2340.2660.2978-0.3762-0.03130.244-0.2827-0.0020.00020.3174-0.0086-0.07480.22120.00790.203214.396730.465-22.7724
20.2989-0.3618-0.29440.56520.06370.4526-0.0528-0.03930.0105-0.32630.0379-0.0496-0.2812-0.106-00.1813-0.017-0.04580.16070.01250.166216.770930.4066-18.8517
30.14850.091-0.16110.0902-0.03640.2610.5248-0.02830.5723-0.4210.3050.9185-0.2110.0673-0.00120.34480.0036-0.09970.12380.12670.47263.719213.7292-18.803
40.1820.01980.26790.1168-0.00820.3493-0.1963-0.7358-0.3345-0.16050.27120.8067-0.0924-0.42020.00030.21290.0652-0.07320.3449-0.02730.34882.000424.2819-17.4241
51.00910.7550.950.46350.57220.6267-0.16660.21160.1139-0.3140.12290.2414-0.2561-0.1846-0.00010.23860.0162-0.00730.17570.01540.21313.890330.9532-21.2157
60.31970.08820.22860.06720.0850.52-0.176-0.31530.49470.39020.4071-0.33610.1408-0.10410.00130.1976-0.005-0.00580.1672-0.00320.199613.919619.6381-8.8646
70.1781-0.32790.1670.3206-0.15530.0934-0.0862-0.0794-0.2460.01780.27530.16050.22350.2551-0.00040.2540.0797-0.0320.26830.03190.275914.2452-8.96315.769
80.9355-0.3270.75820.3167-0.40120.5366-0.0378-0.1035-0.1634-0.03490.0785-0.07630.17260.10850.00010.19610.0320.02290.1583-0.00450.198212.4239-6.9914-3.4023
90.06820.0357-0.04890.0402-0.05490.0704-0.12380.05030.259-0.7351-0.4293-0.39260.71550.6285-0.00170.260.17270.03190.74580.35150.42427.8633-6.09460.3576
100.0688-0.0740.01910.07320.10320.2813-0.0491-0.1224-0.3939-0.4666-0.0865-0.48580.24170.22270.00020.15220.05060.05210.287-0.0120.218217.9787-3.2491-7.709
110.22430.3681-0.05570.3708-0.16470.1955-0.10680.04560.13410.17110.06070.06490.0025-0.03990.00010.21420.0461-0.07760.2126-0.00090.269612.9991-12.84182.7928
120.24590.0527-0.09110.649-0.26020.0908-0.23470.21380.27970.17480.0622-0.133-0.29590.30110.00050.232-0.0097-0.02260.19360.01570.215614.28995.8985-1.9386
131.69510.7619-0.65880.3494-0.27633.43690.06680.75350.8887-0.17050.68420.0208-0.57150.30760.30060.2518-0.0284-0.07640.33140.02840.10830.16023.5741-20.3687
140.8738-0.14890.72610.41540.2110.75530.06540.0409-0.08080.0229-0.044-0.00240.16220.0225-00.181-0.02280.00370.1575-0.02020.14721.5603-5.8595-13.5696
15-0.0014-0.0582-0.02390.13680.14190.1017-0.1838-0.1259-0.16580.1818-0.29960.29880.6459-0.64130.00040.3159-0.06760.03690.344-0.04660.2172-11.1658-4.03871.2136
160.26570.2537-0.27460.6192-0.10680.32730.0753-0.26330.2999-0.2848-0.06270.23260.2408-0.2876-00.1368-0.0247-0.07560.1748-0.01510.209-11.8475-2.3769-8.2496
170.4090.3086-0.10680.4147-0.32850.3122-0.0920.0452-0.2482-0.05150.01470.27380.06950.0445-0.00010.24320.0086-0.02890.2198-0.02990.2195-1.0201-5.0532-16.2379
180.32880.1705-0.3790.43670.14040.5998-0.1341-0.14290.41210.0597-0.0160.2395-0.3464-0.18420.00010.20140.01330.01660.2047-0.00360.1834-1.19226.4704-3.2515
191.05940.63840.1730.55790.33930.6887-0.01440.5793-0.6462-0.15050.0512-0.54360.2227-0.41920.04070.15160.05090.08650.3411-0.12180.206329.229111.7772-25.2256
200.10090.1176-0.10670.1268-0.11530.0573-0.52150.0230.4895-0.09770.4169-0.7835-1.01820.0738-0.0011.098-0.1592-0.01610.7482-0.00230.350628.150828.1271-30.2821
210.2279-0.33220.08130.5377-0.16090.34160.0010.1031-0.1956-0.17730.0915-0.13810.07270.16080.00010.1466-0.03950.05270.174-0.05040.1727.319116.9554-20.0015
22-0.00180.0444-0.03290.0711-0.05270.0323-0.5064-0.2076-0.0177-0.81230.1972-1.0520.17090.95010.00140.46020.07890.13180.5653-0.02580.578642.354816.3103-20.4422
230.66240.5473-0.25361.03570.67420.7652-0.0540.2267-0.1279-0.31190.1836-0.2388-0.29880.133400.2392-0.03090.08060.2419-0.08840.245131.061216.9559-23.8806
240.10080.0710.14180.15840.03450.2058-0.12470.060.14340.06490.2095-0.1237-0.04270.094200.218-0.0126-0.00630.2076-0.03750.210728.507619.7904-9.3849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:19)
2X-RAY DIFFRACTION2(chain A and resid 20:48)
3X-RAY DIFFRACTION3(chain A and resid 49:57)
4X-RAY DIFFRACTION4(chain A and resid 58:75)
5X-RAY DIFFRACTION5(chain A and resid 76:94)
6X-RAY DIFFRACTION6(chain A and resid 95:114)
7X-RAY DIFFRACTION7(chain C and resid 0:11)
8X-RAY DIFFRACTION8(chain C and resid 12:60)
9X-RAY DIFFRACTION9(chain C and resid 61:70)
10X-RAY DIFFRACTION10(chain C and resid 71:79)
11X-RAY DIFFRACTION11(chain C and resid 80:93)
12X-RAY DIFFRACTION12(chain C and resid 94:113)
13X-RAY DIFFRACTION13(chain D and resid 0:5)
14X-RAY DIFFRACTION14(chain D and resid 6:46)
15X-RAY DIFFRACTION15(chain D and resid 47:57)
16X-RAY DIFFRACTION16(chain D and resid 58:77)
17X-RAY DIFFRACTION17(chain D and resid 78:95)
18X-RAY DIFFRACTION18(chain D and resid 96:113)
19X-RAY DIFFRACTION19(chain B and resid 0:12)
20X-RAY DIFFRACTION20(chain B and resid 13:24)
21X-RAY DIFFRACTION21(chain B and resid 25:59)
22X-RAY DIFFRACTION22(chain B and resid 60:69)
23X-RAY DIFFRACTION23(chain B and resid 70:96)
24X-RAY DIFFRACTION24(chain B and resid 97:113)

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