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- PDB-9g48: Staphylococcus aureus MazF in complex with Nanobody 6 -

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Basic information

Entry
Database: PDB / ID: 9g48
TitleStaphylococcus aureus MazF in complex with Nanobody 6
Components
  • Endoribonuclease MazF
  • Nanobody 6
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
: / TRIETHYLENE GLYCOL / Endoribonuclease MazF
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14353600683 Å
AuthorsZorzini, 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 15, 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 6
D: Nanobody 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,20211
Polymers60,3704
Non-polymers8327
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-49 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.140, 60.140, 246.240
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
Components on special symmetry positions
IDModelComponents
11D-322-

HOH

21D-338-

HOH

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Components

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Protein / Antibody , 2 types, 4 molecules ABCD

#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 6


Mass: 15232.658 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)

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Non-polymers , 4 types, 188 molecules

#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M CdCl2, 0.1 M Na-acetate pH 4.6, 30% (w/v) PEG-400
PH range: 4.6

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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 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.14353→39.7614 Å / Num. obs: 28443 / % possible obs: 96.8 % / Redundancy: 2.845 % / Biso Wilson estimate: 48.2159587816 Å2 / CC1/2: 0.995 / Net I/σ(I): 6.6
Reflection shellResolution: 2.14353→2.28 Å / Num. unique obs: 4525 / CC1/2: 0.463 / % possible all: 82.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14353600683→39.7613289734 Å / SU ML: 0.333261603839 / Cross valid method: FREE R-VALUE / σ(F): 1.33786595283 / Phase error: 25.8905696562
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245384553422 1424 5.00650423654 %
Rwork0.216028462864 27019 -
obs0.217533490853 28443 96.4398331808 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.5208165254 Å2
Refinement stepCycle: LAST / Resolution: 2.14353600683→39.7613289734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3625 0 22 181 3828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003342164029963756
X-RAY DIFFRACTIONf_angle_d0.5398648125295089
X-RAY DIFFRACTIONf_chiral_restr0.0447988882359580
X-RAY DIFFRACTIONf_plane_restr0.00442105461867656
X-RAY DIFFRACTIONf_dihedral_angle_d11.33348290172242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14354-2.22010.3839737493531400.3364948654822646X-RAY DIFFRACTION96.035849707
2.2201-2.3090.3317686225311430.3042645465192704X-RAY DIFFRACTION98.2401656315
2.309-2.41410.310715856341410.2804934317792683X-RAY DIFFRACTION97.8516978517
2.4141-2.54140.2793352995611420.2638439137882700X-RAY DIFFRACTION99.058905542
2.5414-2.70050.3158460336091450.2398690102792760X-RAY DIFFRACTION99.3162393162
2.7005-2.9090.2547348179981440.2274528049772729X-RAY DIFFRACTION98.6607142857
2.909-3.20160.2295809797341430.2079600262732716X-RAY DIFFRACTION97.3773841962
3.2016-3.66460.2503975491251400.1916072456442666X-RAY DIFFRACTION94.861392833
3.6646-4.61590.1946256031021430.1698292346422720X-RAY DIFFRACTION94.6759259259
4.6159-39.76130.2423948960651430.2292461020772695X-RAY DIFFRACTION89.2452830189
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.105677181481.379153693113.915662806930.6297076589391.520989438234.93934211266-0.359179334137-0.285509127352-0.2072409890680.507322985119-0.2576880691261.523192325650.902934913624-1.205658531190.05706868808690.530761919776-0.2244146761050.1779782718720.643989501622-0.07518278414120.7910012303537.522963521090.46268627716120.5281605417
26.39280281083-0.20792594236-0.4103947090346.15412155234-0.9501977774918.454605002450.0902138364780.0980515985089-0.3716444591451.15361452537-0.4365085311160.568218395457-0.655236083272-0.4639901844170.2781936584020.58152971936-0.0515029361040.1387445612910.443709894071-0.1210420583030.54509652557710.8761451833.5771798742811.9091535239
33.537463237470.6834912008412.938666294273.685223786872.275708576183.09882822722-0.7737498544870.455099889172-0.8866253672291.44557657365-0.0808922037230.7506697074630.09299038696080.9549768831380.5176891657091.09174784567-0.1715368546460.1976739276340.8751668410260.05400863660140.91460469394213.890584441917.68233976317.01974947702
42.83056945344-1.964655512260.9736788032022.035681192560.6935013172472.343317894110.1206882467450.0750889597804-0.663965683484-0.471058844414-0.38504210169-0.120357403138-0.7141241208350.4893986387430.2061891139780.513274035109-0.07213054479940.0861560983770.424821319809-0.02094314239720.40175469205412.77201704597.3686080869416.1226651491
51.70671256504-0.789083147079-0.6378754981922.772719815941.249589099042.94449075750.04816615959890.126676002185-0.159862241792-0.2065362090960.0501790244075-0.0564497406036-0.09517268208510.005765851030710.009537456473250.441418857886-0.09858925815580.001966527522770.327595892684-0.008154617349960.28683141652315.73979764418.9876938057417.8293689904
60.320952990365-0.2048935456470.6154833381270.347158682348-0.3279476497011.472911203060.102851848259-0.202165680664-0.125438443877-0.901351001770.2641888065711.040141484390.3248920623140.271068750279-0.1495524987730.646278287032-0.116764167721-0.07811050234440.4484103498310.07462525125870.63685164761426.04993798641.1078630186414.2232123384
71.50031294556-0.268761195376-1.866113997520.9424843116241.988608809281.41846587236-0.2727359728470.6277406651290.381927835323-0.2995432354710.388257352672-0.2666268450560.101512327352-0.136986369451-0.09945661047160.473943652623-0.1260396597450.06934201412980.4607032563790.01254716947490.34889140833315.90980633188.7952174026712.9404193251
83.22389600524-1.59948101529-0.2881279557634.66630888311-0.3103351264143.08284447153-0.07002205471450.06011263960480.0867220838545-0.524227511987-0.422139713033-0.1923614743270.952715557379-0.7012180333090.5338113701080.617826285975-0.2103196696260.05209569907930.446313663457-0.03158093422660.57692629669513.4227554421-1.3821110850714.5017998359
93.19921533294-0.4791889201971.173370414322.602798705412.001477156982.116439871170.194151182717-0.6085154943460.04095061315050.586035574369-0.20890002193-1.472878171810.2515885364120.2457861996-0.05639092016330.455273584653-0.1264894115390.01255228140580.5003318784360.05181453298660.42225770072522.58958508656.9814693173225.5505696079
109.74824552621-2.24251741201-3.482199179362.86638150892.438714287052.35482496256-0.544048090591-1.344174703270.6196255485431.39975285289-0.760067496393-0.968635794095-0.2670268621840.984014840793-0.07460162711670.855613989508-0.17909234632-0.01814695808110.7111870879520.01618436750730.56467246872520.793924476618.373499774730.4675534175
115.76084466436-1.753371890012.464621564662.5560889777-0.07546880541286.18626196222-0.314424617166-0.0105597293840.5299383740490.2211426602120.09955988308310.129437069496-1.371596154050.5149178490970.1348669620420.650424260461-0.0699591568870.03580683026670.4645380560670.0297557421510.4745114679515.358550270831.273090749522.6257933827
126.746794086811.78457366036-1.097260877516.90915659972-1.906158944560.568448883730.289916996742.153953081240.311944889381-1.05855158218-0.2743363017550.4512427217881.3130552533-2.81227078562-0.3199793560871.22952825977-0.1823383027890.008127268153141.167821039730.001250917945450.8970929405123.5407418220923.0396627212.9827314574
133.97863448026-0.0665466817592-1.601101775861.661462726751.404628997941.027818600590.1136171787670.09786965870450.251485604386-0.15378140074-0.0177102586355-0.0389238383689-0.326044199472-0.0313902944490.04904421972340.40880364344-0.04898515484630.03206516965110.4464968628550.06396501638970.36645379835111.728360584723.821230207723.4741757947
143.589467994310.6597624833332.372521399280.9978844868251.437128276964.07047448693-0.804851120427-0.3165400028330.8245128116320.746574503857-0.009370478989110.584651076206-0.6061333609930.1276081081470.4341720901720.6797026840150.031623438005-0.01861313954040.463900540731-0.02374942380520.6873853760721.9811586429831.095400538531.5417623615
154.832377708950.703044377016-2.13251507330.977914836031.013877768542.94422131622-0.2586784622960.699711400487-0.571825860706-0.568883258245-0.1657139472510.06955042217190.0193819324859-0.5015813619060.4255749748360.56126477534-0.07884516596670.02207433849250.373355714109-0.02069246122240.3841559412819.6202661890322.638075030519.370985653
162.38627813878-0.3492861575751.100957126123.07234997542-0.693151048130.1333366837590.197787207406-0.3486085542540.4868708601580.486253640525-0.328879334843-0.225890895257-0.2452309846980.08626429329870.1273092660870.435525514169-0.02878330524130.08092801046860.4154915180260.02638389502180.43578126586512.226102535725.811762262229.9808861699
170.1108470046430.298067774235-0.5292882390012.12684715692-1.303600206631.68714046319-0.144929816808-0.496495830051-1.175128553580.84335886969-0.7466536698110.1563758125320.455019070560.9329955172190.711756960280.460357238332-0.0732348619570.1391220654770.6718558063950.03975740071770.57945711544314.46141903847.5181984529132.1732880874
181.875644419421.678753830420.2408629166943.291053876372.266627752432.42732432192-0.1236513569240.4698093790640.153931516107-0.5717316221430.371244105841-0.496720919201-0.4814747005180.346916404747-0.1353903369210.467357699857-0.0856024245630.06008832705860.479691539249-0.01045738424030.54001926011251.056735204331.805871123811.9701450698
193.723803328630.486698090491-1.479405911123.73555421950.4793227319022.04011190707-0.0817091467476-0.253150652533-0.08895023943650.534626208606-0.01573580878010.07481801033470.431248186809-0.155309771027-0.03383905063180.678136830772-0.1005745973710.07944576343580.4974172350460.01918043416020.54548062594541.503760671324.332405503313.0050928597
204.29050703554-0.358802195048-3.449145914371.52228873542-0.2582179250632.901449620750.2687418186940.7832926818541.075024128790.197410553209-0.4123348192540.9962157173770.766515967703-1.657968331960.5649218919830.561295065105-0.0383272777710.06303464433180.683472214222-0.005376687373130.70537711857332.699290745729.45802498376.86312031415
213.669270037832.7401744401-0.004075718001967.842694010292.980826184786.21770844448-0.2658544302650.2881446779060.4176699472180.02508455782520.136024580560.1510330019580.290132086215-0.5261630290840.2544534114820.455866117915-0.08227461397350.05882143751320.360294154024-0.01232255690660.4032371055842.037246227232.74920395237.71993411283
222.169744795462.505202956330.2159732690931.32445020223-0.3466183483070.7214868949210.2768486304520.05732938772290.08629856993410.326804646732-0.208331073570.1756823978590.00935280832294-0.2588078712320.06309123317420.530045285024-0.09702641507440.1086857371740.536101749085-0.03845527938810.46135525989338.404428105926.241513011813.4883337421
231.812704981331.157379675870.6734961999344.914480630230.9099998570312.299709513630.148249728868-0.244967338132-0.6243908890310.660945297359-0.00802699538667-0.490761122630.3451090100590.12178793170.1646906411170.559183581926-0.09438904090830.05794933808250.525969710948-0.01023479451390.50253199521643.989044664522.288105649716.359990204
240.3434302155330.8848389138530.6827167288661.09745360430.3617933464571.19573226707-0.1447256822081.219204765840.4481305308210.309235676823-0.1262165615691.95874030164-0.206726711586-1.110455418920.03990371267540.559558493817-0.06100031197860.1247333368110.524834090871-0.01984321506670.61249560554-20.5301158482.040474977739.9437786923
250.705828895968-0.108978646182-0.8849662717670.8409467697670.04932919747532.11435394347-0.2258002116950.2219868571560.13445417362-0.1072222944810.1816764015370.0322605586428-0.178865388253-0.1250424341320.06716771013360.419146092776-0.0897051038726-0.01753473948530.4933349626410.03875264750730.499040589081-14.45817033073.8440008836833.7313785727
260.5844422630010.0850832078604-0.6321615922262.144004058331.586101077711.90371688253-0.273697443140.6884431487320.56697121069-0.493834340475-0.423551917028-0.0208882283631-1.914900296910.5759509081030.4030333985430.947091095235-0.189897074298-0.1204106437340.6391987272190.120361684570.567386331066-12.36714862266.4690718119921.8522106764
273.189473743430.203023778169-1.600705980815.669522612790.9918460790522.953553160120.0119257631630.726050776476-0.00466306439695-0.613492622565-0.1391506410890.2577051102720.17731988819-0.5686487902330.0309532275510.466238846114-0.1054502793190.001436651308530.645833488855-0.04351966647190.476703571367-18.68040693241.34514057127.7969505492
281.891995480972.41205139628-0.4134750397151.88273617424-1.28085595724-0.6521919124950.008215699455270.1333304801820.012888589793-0.190464680654-0.05204057716830.2633256236290.1489651779260.0301770880460.05448019847250.446896809185-0.06591479750330.0183973606810.4952829951530.008897154427710.447898616307-10.07505423437.1592526268932.6814145403
293.992047675861.234576807622.047696345162.74179521311-1.312377546332.844723777720.576856402613-0.300913124982-2.214524849930.563820170218-0.7834031409360.2841724110311.148606556220.1944419973620.2521298368650.6527211704-0.1009228728280.07622666067720.5118292760390.03093636061410.762958139373-15.9298946238-10.817010321142.2754957718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 11 )
3X-RAY DIFFRACTION3chain 'A' and (resid 12 through 22 )
4X-RAY DIFFRACTION4chain 'A' and (resid 23 through 31 )
5X-RAY DIFFRACTION5chain 'A' and (resid 32 through 57 )
6X-RAY DIFFRACTION6chain 'A' and (resid 58 through 66 )
7X-RAY DIFFRACTION7chain 'A' and (resid 67 through 86 )
8X-RAY DIFFRACTION8chain 'A' and (resid 87 through 95 )
9X-RAY DIFFRACTION9chain 'A' and (resid 96 through 109 )
10X-RAY DIFFRACTION10chain 'A' and (resid 110 through 114 )
11X-RAY DIFFRACTION11chain 'B' and (resid 0 through 10 )
12X-RAY DIFFRACTION12chain 'B' and (resid 11 through 23 )
13X-RAY DIFFRACTION13chain 'B' and (resid 24 through 57 )
14X-RAY DIFFRACTION14chain 'B' and (resid 58 through 71 )
15X-RAY DIFFRACTION15chain 'B' and (resid 72 through 86 )
16X-RAY DIFFRACTION16chain 'B' and (resid 87 through 109 )
17X-RAY DIFFRACTION17chain 'B' and (resid 110 through 116 )
18X-RAY DIFFRACTION18chain 'C' and (resid 3 through 24 )
19X-RAY DIFFRACTION19chain 'C' and (resid 25 through 51 )
20X-RAY DIFFRACTION20chain 'C' and (resid 52 through 60 )
21X-RAY DIFFRACTION21chain 'C' and (resid 61 through 83 )
22X-RAY DIFFRACTION22chain 'C' and (resid 84 through 112 )
23X-RAY DIFFRACTION23chain 'C' and (resid 113 through 131 )
24X-RAY DIFFRACTION24chain 'D' and (resid 3 through 12 )
25X-RAY DIFFRACTION25chain 'D' and (resid 13 through 51 )
26X-RAY DIFFRACTION26chain 'D' and (resid 52 through 60 )
27X-RAY DIFFRACTION27chain 'D' and (resid 61 through 83 )
28X-RAY DIFFRACTION28chain 'D' and (resid 84 through 124 )
29X-RAY DIFFRACTION29chain 'D' and (resid 125 through 133 )

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