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- PDB-9g5z: Nanobody-mediated activation and inhibition of Staphylococcus aur... -

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Basic information

Entry
Database: PDB / ID: 9g5z
TitleNanobody-mediated activation and inhibition of Staphylococcus aureus MazF
Components
  • Endoribonuclease MazF
  • Nanobody 11
KeywordsTOXIN / Toxin-antitoxin system / Ribonuclease / Nanobody
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
mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor
Similarity search - Domain/homology
Endoribonuclease MazF
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4290937208 Å
AuthorsProlic-Kalinsek, M. / Haesaerts, S. / Loris, R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Vrije Universiteit BrusselSRP13 Belgium
CitationJournal: To Be Published
Title: Staphylococcus aureus MazF in complex with Nanobody 11
Authors: Prolic-Kalinsek, M. / Zorzini, V. / Haesaerts, S. / De Bruyn, P. / Loris, R.
History
DepositionJul 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoribonuclease MazF
B: Endoribonuclease MazF
C: Nanobody 11
D: Nanobody 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5447
Polymers57,3244
Non-polymers2203
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-15 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.100, 102.100, 101.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNPROPRO(chain 'C' and (resid 5 through 12 or (resid 13...CC5 - 434 - 42
121GLYGLYSERSER(chain 'C' and (resid 5 through 12 or (resid 13...CC46 - 11845 - 117
211GLNGLNPROPRO(chain 'D' and (resid 5 through 20 or (resid 21...DD5 - 434 - 42
221GLYGLYSERSER(chain 'D' and (resid 5 through 20 or (resid 21...DD46 - 11845 - 117
132PROPROASPASP(chain 'A' and ((resid 0 and (name CA or name...AA1 - 10314 - 116
142ALAALAASNASN(chain 'A' and ((resid 0 and (name CA or name...AA105 - 113118 - 126
232PROPROASPASP(chain 'B' and (resid 0 through 66 or (resid 67...BB1 - 10314 - 116
242ALAALAASNASN(chain 'B' and (resid 0 through 66 or (resid 67...BB105 - 113118 - 126

NCS ensembles :
ID
1
2

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Components

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


Mass: 14952.206 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mazF, SA1873 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7A4G9, Hydrolases; Acting on ester bonds
#2: Antibody Nanobody 11


Mass: 13710.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.01 M Cobalt(II) chloride hexahydrate, 0.1 M MES monohydrate pH 6.5, 1.8 M Ammonium sulfate, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.4290937208→45.574579877 Å / Num. obs: 8391 / % possible obs: 98.6 % / Redundancy: 9.9 % / Biso Wilson estimate: 107.190656778 Å2 / CC1/2: 0.995 / Net I/σ(I): 8.14
Reflection shellResolution: 3.4290937208→3.64 Å / Num. unique obs: 1237 / CC1/2: 0.372

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4290937208→45.574579877 Å / SU ML: 0.542376142696 / Cross valid method: FREE R-VALUE / σ(F): 1.35108234315 / Phase error: 33.2416431123
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.283114662681 420 5.0107372942 %
Rwork0.244334367676 7962 -
obs0.24628427461 8382 98.4958871915 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 109.132728044 Å2
Refinement stepCycle: LAST / Resolution: 3.4290937208→45.574579877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3415 0 13 12 3440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002812924815093503
X-RAY DIFFRACTIONf_angle_d0.8301952784924775
X-RAY DIFFRACTIONf_chiral_restr0.052814820104546
X-RAY DIFFRACTIONf_plane_restr0.00449526773557612
X-RAY DIFFRACTIONf_dihedral_angle_d11.91348548572064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4291-3.92510.3522446580331340.2783830835442540X-RAY DIFFRACTION95.6708407871
3.9251-4.94420.2564857887791400.2258781947542659X-RAY DIFFRACTION99.9285969297
4.9442-45.5745798770.2798385089231460.2445657159862763X-RAY DIFFRACTION99.8284145504
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)
17.489505912450.8726835192810.01282943008598.223612524391.555150372786.97182968550.0997299356223-0.0190694308880.07110460077010.675557874038-0.09319224452270.02856223169760.377562422092-0.185435442091-0.07782801912940.5591556325390.005836741911540.04627601049250.697648317751-0.01368976086010.60836363175621.18352743083.120037218510.990832229007
24.370921756350.900764777649-0.1715454877676.54658080721-0.08330811533857.733466624470.4065923073980.4981699649520.3518952175080.394088760117-0.020682674451-0.384008313415-0.786999300360.334388708586-0.4552717178240.842714205905-0.0948966277991-0.008427240659590.91185691159-0.06472297386670.75084948863432.959921929918.4967982878-5.23823719673
34.45213083392-1.51588274273-2.766967963157.39341494348-1.973563236947.135536839160.180144291922-0.246848999828-0.3982375993480.268721252309-0.234798712359-0.07158864547360.3216420855370.534074990224-0.01326904628990.984364737351-0.04884972553560.001509888305850.703458780663-0.06195612578360.62206563050331.0715278482-10.203956885928.1826698389
48.03146390091-0.440862910464-4.777730313592.15643055326-1.817159310016.893471585950.02132210799790.26762836353-0.145290140488-0.08143019158140.002381078133750.3579406330460.0535288445115-0.0187783361505-0.07900040126830.940877786439-0.345126709548-0.01742796621051.40816209640.01098341769290.97780451993952.02804486111.1368328419-28.7101198147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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