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- PDB-9g2g: Staphylococcus aureus MazF in complex with nanobody 5 -

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Basic information

Entry
Database: PDB / ID: 9g2g
TitleStaphylococcus aureus MazF in complex with nanobody 5
Components
  • Endoribonuclease MazF
  • Nanobody 5
KeywordsTOXIN / Toxin-antitoxin system / Ribonuclease / Nanobody
Function / homologymRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / Endoribonuclease MazF
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.80048236056 Å
AuthorsProlic-Kalinsek, M. / Zorzini, V. / Haesaerts, S. / Loris, R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Vrije Universiteit BrusselSRP13 Belgium
CitationJournal: To Be Published
Title: Nanobody-mediated activation and inhibition of Staphylococcus aureus MazF
Authors: Prolic-Kalinsek, M. / Zorzini, V. / Haesaerts, S. / De Bruyn, P. / Loris, R.
History
DepositionJul 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 5
D: Nanobody 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6785
Polymers58,5564
Non-polymers1221
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-25 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.600, 50.873, 52.083
Angle α, β, γ (deg.)67.502, 79.804, 85.349
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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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 5


Mass: 14325.571 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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M TRIS pH 8.5, 30% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.80048236056→46.9961366314 Å / Num. obs: 34576 / % possible obs: 78.8 % / Redundancy: 2.65 % / Biso Wilson estimate: 23.6616470756 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.55
Reflection shellResolution: 1.80048236056→1.91 Å / Mean I/σ(I) obs: 1.78 / Num. unique obs: 2227 / CC1/2: 0.917 / % possible all: 34.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.80048236056→46.9961366314 Å / SU ML: 0.228991376352 / Cross valid method: FREE R-VALUE / σ(F): 1.9613439742 / Phase error: 30.0478257331
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.243854432982 1596 4.94960458986 %
Rwork0.195452200843 30649 -
obs0.197811004035 32245 73.7062265704 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.5688336135 Å2
Refinement stepCycle: LAST / Resolution: 1.80048236056→46.9961366314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3540 0 8 304 3852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004438837291323723
X-RAY DIFFRACTIONf_angle_d0.7454533381165080
X-RAY DIFFRACTIONf_chiral_restr0.0520552466107571
X-RAY DIFFRACTIONf_plane_restr0.00435837058659
X-RAY DIFFRACTIONf_dihedral_angle_d14.60074880782251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8005-1.85860.343070169533290.335308620119744X-RAY DIFFRACTION19.325
1.8586-1.9250.402408291016580.2909448605051070X-RAY DIFFRACTION28.5497342445
1.925-2.00210.287445532889950.261746812311515X-RAY DIFFRACTION40.6873894364
2.0021-2.09320.3045981595441090.2533989798032384X-RAY DIFFRACTION62.3717788341
2.0932-2.20360.286980716771500.2379227185453172X-RAY DIFFRACTION82.7397260274
2.2036-2.34160.2775468659351930.2304144621233409X-RAY DIFFRACTION91.5607524148
2.3416-2.52240.2946855503391920.2277867076933649X-RAY DIFFRACTION96.7019133938
2.5224-2.77620.2686056471142080.2258815560413646X-RAY DIFFRACTION97.2495584153
2.7762-3.17790.2732053476442100.2128089502633705X-RAY DIFFRACTION97.4365355898
3.1779-4.00350.2209640480931770.1701984718373659X-RAY DIFFRACTION97.1631205674
4.0035-46.99613663140.1747827760251750.1458616499063696X-RAY DIFFRACTION97.3346743777
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)
12.14693308959-0.1635142725340.1403768992616.954718942830.5440255153116.7306541672-0.320787898791-0.647739554132-0.2011339023030.1089257810660.301985510973-0.9052577099680.6702840684720.9320940750890.01329678154180.3425733133350.100199062384-0.03031211673530.2906898731750.007503393873040.3162453562210.792382284112-14.1498283042.399250187
29.43310285494.790298361075.615063792545.70885195797-0.3960221176246.56011118260.1454094940170.8012651066990.0555374731309-1.022747309760.229447314119-2.63110243844-0.124221506262.73490501864-0.3288021483150.633931659187-0.09701470286510.3474178278410.698448492165-0.1669315951891.158334950866.995047638992.33549975521-1.79519419489
31.61328593222-0.867568118974-0.1262205996711.384833358250.4391492773891.87585919436-0.165121293074-0.454666562302-0.06519343007350.3693740598460.37094760493-0.0796261627440.2400601772260.100110482291-0.1401784105470.172004381738-0.00128821187423-0.01353139344050.1800552242070.04627854076740.135546455377-6.96608729804-7.901070301812.96751270128
42.70507768718-1.55155262855-0.5725700188091.177190865061.043972489272.29877298838-0.0792425331958-0.69100041176-0.03286572356040.2966141176580.439246669409-0.2652634167040.002945112376410.468437636023-0.2625783368370.1747881804270.0147864838309-0.03738672749280.282944304721-0.005017818024060.221372714411-2.99066283185-7.066265195324.50327807199
50.8668311084830.458808983455-0.5127017424063.2673258442-2.158040837814.87502966754-0.00225117151203-0.455784982662-0.5615308098280.331264284081-0.1185129528990.04196429333530.554592298793-0.0480177155574-0.1827892510560.229772112001-0.08219548143460.1218315118920.2418951013260.2372927924040.296308944752-17.4406206304-11.71576256351.03814739652
64.44064703920.293554156552-0.05057233593484.77566035187-0.3281639358083.761963522430.1300998027740.3851813332980.86189797398-0.42308047657-0.05013004358930.0589365405245-0.8085636338-0.0872991333568-0.001529930820350.2995984419620.03781644932220.02827449233860.2112155307590.06654186698630.233607984844-19.12808070975.74574509627-17.3693645847
76.53772224272-6.46514060083.294680385589.9061277707-0.6013492021173.669530719510.0362595232973-1.462314001911.670177635551.02236808345-0.591381059219-2.81694747328-0.6386280232361.955652338570.509110472640.356528535478-0.230332751733-0.003970069278921.01902161293-0.04856177661120.893782681809-0.803651040293.93722044087-14.4470816957
81.255279441060.230334599682-1.212147705933.7225031185-0.881630702944.03229706650.008861990661970.06569538686130.0206124713699-0.4261275964390.0226621364392-0.256663259666-0.316079644810.2916339747180.4189829009810.164227096264-0.1776993134020.08371815582820.09476898229630.08703756049390.0734701979553-12.8992067901-1.01287883275-15.5416668558
91.86415497639-0.883747826719-0.4958205409721.808490262650.3852604546461.355855226070.2365018009180.01352059991580.1288418222640.0280142706886-0.151596822466-0.0910282181394-0.065535834252-0.1082673810150.03474934292050.0531207253893-0.07859332366650.086745681040.1303211460180.07129591509340.0517128177297-16.76239880311.53399999015-10.221598664
103.73348341990.373419348367-3.41755034348.33928522996-6.351106991068.669880997660.4210183010840.679030009221-0.255219593321-0.383234325316-0.4848157352290.01410840132780.03910032229370.1592493761580.03136687052580.1907394110540.0317029687922-0.02304834152670.25352917544-0.04348691043350.128904391583-4.81520825293-13.9405825313-23.1320111518
112.26418747456-1.689790597733.103478026082.13654176111-2.214110010724.275016827240.4688983888150.7665531063530.0822043478669-0.621311797478-0.447493923506-0.080071443282-0.225397634603-0.104706851828-0.05134680999590.3527424530350.1901765411050.003954161575670.4448025683390.006294590727630.14405688019-13.0527418388-7.49557265865-28.396225665
120.888990271112-1.52589128940.1639535180993.738882840350.7265063158970.9346771660250.1452795007580.1203467924950.348558162744-0.105078009706-0.138533732777-0.45008101934-0.3270893604360.367511411555-0.05407690712230.127714194138-0.09160247281790.05376324526680.1965433175240.01125683248070.22041079582-8.70674496266-1.16779449909-13.3281632609
135.274506081332.303879507332.93845291799.487776999963.536734889026.23053868790.04547086823980.9371687755870.377837297637-0.757652331654-0.0567766282368-0.0120403928126-0.7323516974850.1444881723440.03817537485810.255814797740.05632712328980.02859269467020.2613322343790.08047850799930.143010815724-17.71633035911.85816025563-21.8632421142
144.38851457635-1.14454988111.954863757631.69587655647-0.6789144291326.038990457490.139718347920.119863908652-0.467744370283-0.015312570518-0.1171423992690.5910085535410.44354431103-0.628598387631-0.02578883616530.202599692865-0.122328315771-0.02519028962450.154809320102-0.09473306672520.373775157706-17.2630428069-14.4780845079-13.1987273406
152.87715446191-0.930668977143-0.8627777715811.889259220690.9037509343180.6442768972240.5343291449390.905845213904-0.200131447449-0.69691271927-0.366960868365-0.158258749979-0.0673324811531-0.275561342592-0.1027513127880.6314327933680.379570134569-0.1742734911410.637684252496-0.2028487473020.42238794352613.785658338-36.0034784135-25.4396234236
164.363131557670.8790550883180.9673018273729.33375874592-1.301669501453.338462345080.4131306966120.966438716135-0.109329686199-0.270250095683-0.106130560463-0.6532111495950.4315435119720.668344055386-0.1419169677230.2799553567830.188912190378-0.07395137305090.466988014051-0.04320919852990.2983156578788.15775076245-23.0892561536-25.2466366643
174.026925227430.234516491019-0.2858654032683.163002820930.8075896672835.206404731130.2105248201320.461871835069-0.57307002211-0.01018402367010.1071017628060.4680163337870.595472460881-0.0622582336632-0.2858966509980.2699285637410.0366299166116-0.1119607026660.234987830492-0.00237608442430.3004277356313.87363676414-29.5313393848-15.9914288634
180.150469143666-0.4840053382170.6350823495895.72722548952-5.664207516425.822267046860.05179749238180.4927521194470.0615258595831-0.137614568377-0.551281130378-0.957411463385-0.171864691950.8024927314730.559612536360.36543832030.1376697384060.003357164474360.508003495889-0.006266831251080.44793478137216.4430945618-24.470457028-21.9943042501
193.10072809436-1.019781435631.436012509432.207558374141.583468164712.921685223070.6348915169080.47886668619-0.648873978309-0.219193125216-0.1905997089010.07987225810630.542531706125-0.17588178604-0.3030722068820.4626325665120.148550967665-0.2627079217440.354492968136-0.1304161565060.55402057733511.6813743053-36.9350648359-18.7272940456
201.05373604413-1.52870629274-0.6905649162723.982347319190.4122570843610.6679679530070.6366755444860.582627038984-0.502970374997-0.417711543337-0.2764127931440.08971980037810.5278523117060.126183012166-0.05538512582450.3749939310890.134278372467-0.1936487472070.327547393049-0.1115716226410.3532355084143.44751752794-27.0162941993-24.4353973834
211.756941751020.7281063184831.068197336350.3672430616220.8485877389153.15443817754-0.173946838533-0.4003549242070.1773132147040.300471269770.193013538071-0.2316158978780.3122771520450.143118063598-0.398214670140.4455242527790.238912241354-0.2232594021460.642486800683-0.3648596512140.450987622702-23.083527245218.224548574217.975650664
220.505083482133-1.065460059381.190492354522.34868986302-2.015809737545.19635395845-0.0801332461843-0.3089088443270.6654408405290.2410770182250.563645826894-0.582778560266-0.389194631017-0.265573296035-0.1877420892340.3496510937660.149467611794-0.04883443802740.301866070744-0.157054890180.394697693704-37.087741006623.77957868979.28227093928
234.089890644531.340421386971.615503449416.732677704031.556699203921.86090391096-0.130986325602-0.2896215639170.3061449819280.1264437537340.22664393691-0.62459908704-0.460468229070.413102624783-0.2264911694220.449626262811-0.118703251796-0.02336517972820.740646350048-0.4863090829950.926896844921-15.612954359319.289892990710.2377703646
244.004378411372.0229960566-4.820865092253.60285597856-2.062539200365.86009997132-0.380945907772-0.214328403047-0.1272627333530.2493449600340.350556919159-0.1253913924990.0541264973467-0.2883449501730.008282084675080.1849492832130.06634994161840.01449299434420.2597281051650.03460631076410.138373571305-32.27226930819.88580970418.58332835306
251.37359953602-1.23309480969-1.792795379192.74998959319-0.7037167108325.6088396551-0.126401906499-0.1051338808190.5214353866260.05811278235760.302944728088-0.234695445061-0.292258923526-0.255414771858-0.09957522869530.184928841107-0.0132634811549-0.04558205050730.161546737669-0.02506773505710.215647124321-30.60125602217.21973788253.86314648375
263.1916607293-2.19319277394-1.742609004892.749886097010.9427311388971.12929091134-0.32195885955-0.636739379980.3496366630860.1768473250790.459645060738-0.162026004042-0.171095128203-0.0936645495553-0.1557246051530.2072725106430.1077635378940.0007635282448640.365733588477-0.0007002549435860.140193035161-26.097158251910.90230554869.92716506978
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 11 )
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 22 )
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 95 )
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 114 )
6X-RAY DIFFRACTION6chain 'B' and (resid -4 through 11 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 22 )
8X-RAY DIFFRACTION8chain 'B' and (resid 23 through 31 )
9X-RAY DIFFRACTION9chain 'B' and (resid 32 through 47 )
10X-RAY DIFFRACTION10chain 'B' and (resid 48 through 57 )
11X-RAY DIFFRACTION11chain 'B' and (resid 58 through 71 )
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 86 )
13X-RAY DIFFRACTION13chain 'B' and (resid 87 through 95 )
14X-RAY DIFFRACTION14chain 'B' and (resid 96 through 114 )
15X-RAY DIFFRACTION15chain 'C' and (resid 3 through 25 )
16X-RAY DIFFRACTION16chain 'C' and (resid 26 through 40 )
17X-RAY DIFFRACTION17chain 'C' and (resid 41 through 68 )
18X-RAY DIFFRACTION18chain 'C' and (resid 69 through 78 )
19X-RAY DIFFRACTION19chain 'C' and (resid 79 through 92 )
20X-RAY DIFFRACTION20chain 'C' and (resid 93 through 125 )
21X-RAY DIFFRACTION21chain 'D' and (resid 2 through 8 )
22X-RAY DIFFRACTION22chain 'D' and (resid 9 through 25 )
23X-RAY DIFFRACTION23chain 'D' and (resid 26 through 33 )
24X-RAY DIFFRACTION24chain 'D' and (resid 34 through 52 )
25X-RAY DIFFRACTION25chain 'D' and (resid 53 through 100 )
26X-RAY DIFFRACTION26chain 'D' and (resid 101 through 125 )

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