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- PDB-9g4g: Staphylococcus aureus MazF in complex with Nanobody 9 -

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Basic information

Entry
Database: PDB / ID: 9g4g
TitleStaphylococcus aureus MazF in complex with Nanobody 9
Components
  • Endoribonuclease MazF
  • Nanobody 9
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: 2.89572919242 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-Kalinsec, 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
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: Nanobody 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7413
Polymers29,6452
Non-polymers961
Water1,33374
1
A: Endoribonuclease MazF
B: Nanobody 9
hetero molecules

A: Endoribonuclease MazF
B: Nanobody 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4836
Polymers59,2914
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area5230 Å2
ΔGint-40 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.090, 133.750, 100.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 14952.206 Da / Num. of mol.: 1
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 9


Mass: 14693.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammoniumsulphate, 0.1 M Na-cacodylate pH 6.5, 30% (w/v) PEG-8000

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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: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.89572919242→46.0840534125 Å / Num. obs: 7201 / % possible obs: 93.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 43.425238765 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.51
Reflection shellResolution: 2.89572919242→3.07 Å / Mean I/σ(I) obs: 2.65 / Num. unique obs: 1195 / CC1/2: 0.842

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89572919242→46.0840534125 Å / SU ML: 0.550017910456 / Cross valid method: FREE R-VALUE / σ(F): 1.35933942305 / Phase error: 30.9558380693
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.303201178834 360 5.00556173526 %
Rwork0.252761150504 6832 -
obs0.255352559346 7192 93.4511434511 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.9482501898 Å2
Refinement stepCycle: LAST / Resolution: 2.89572919242→46.0840534125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 5 74 1901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002165123166561858
X-RAY DIFFRACTIONf_angle_d0.5705545959032520
X-RAY DIFFRACTIONf_chiral_restr0.0439709526599286
X-RAY DIFFRACTIONf_plane_restr0.0037171493906326
X-RAY DIFFRACTIONf_dihedral_angle_d11.40619756871124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8958-3.31460.3956025324071220.3300192790412318X-RAY DIFFRACTION97.1724412585
3.3146-4.17570.3591224361991140.2750969392732173X-RAY DIFFRACTION90.0748326113
4.1757-46.08405341250.2292691143611240.2031078163882341X-RAY DIFFRACTION93.1947069943
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)
12.800682784481.861639488930.7383878733782.244000073181.664894126661.958212384680.188904877638-0.3218057297580.5197474234041.12692691562-0.3948972007560.37848442145-1.20781610342-0.818021792150.2451076858750.9736619576180.1568239881834.01659820895E-50.55859655638-0.1116861991120.30978371418916.9902973532144.54231541112.5126724083
21.53184076912-1.843395595812.30204824933.1425270143-1.35552696355.68650823712-0.4071977653160.2451453419740.0331035005471-0.3300415826010.8578391619590.0835634714232-0.921979539745-0.691668830911-0.1473125016261.31773190245-0.2687821563740.1775243992520.7043436009360.09195856568270.1269618400758.55053886674138.18916449513.8255333268
36.035867330345.293022111636.104101197724.721606570965.717789378378.395673249061.140820598160.386298956128-0.6938232212921.2817974568-0.458553718616-0.1440759626480.4013280259420.701037105425-0.6370246196931.05531829087-0.1071866039480.06509816815941.232051856850.09857089192951.056495648692.03066041267129.026282074.40066061258
45.58134504413.93360353573-3.649736992217.53031870388-4.309223196547.282978113270.2516225160260.2849646483060.1355917192910.56720243170.2844379104690.493575298340.260697190010.0676092057366-0.08338605468720.626039345324-0.0819308221862-0.08395913233550.41490792747-0.1213218024580.23187643510612.5645107466136.5422871839.42862592289
51.82088138746-1.192688017020.05268787820456.961546085830.62776977741.814188277670.1075345800450.139422233371-0.2295100886730.3437601403440.115508069190.51247084875-0.278146811027-0.155245917689-0.1208951462030.5943442578390.02966855613650.009269818869020.302627947478-0.03836429300760.19730827185215.0552395946134.3292458367.69248405277
63.014247286720.474209827472-0.6660793752932.78168693679-1.148249563532.279651887540.126701822133-0.4628961264610.3698471700530.701803121763-0.2828066348680.389540589566-0.0327747852193-0.3328245218180.1919037449210.849794503437-0.0538032194576-0.008096931235820.35631959394-0.05451557715580.36268318195113.107156478132.94258483514.0135895419
73.9751947208-1.846135327831.747923023833.02014249697-1.591195328855.756113110760.0924776939489-0.4938095265860.4550745392570.706317271815-0.209336258342-0.654306835095-0.1886299455450.4348124295130.02350239823480.618595242104-0.0487390254262-0.01937661549820.370510036648-0.04528288423160.34284879482825.9240478113130.4702121516.34682380674
89.5596045397-2.090261855622.425243925772.84668731745-0.457772364895.935421477560.0602920008970.22197553379-0.927377546292-0.595980459066-0.07175618145790.4895228839231.34295638277-0.0154424508446-0.00150525414790.741628963494-0.00600637514585-0.08503596200380.331998122626-0.03905515848860.42766818370125.050300052894.752483214913.3854715629
91.208286855421.38577184379-1.08121141082.89255172535-2.580335155983.93923368595-0.1411181747420.6635857702360.104665677799-0.582906479873-0.1546196423570.112906669170.0673625864406-0.4405913130720.1888686664250.968503829729-0.2685482500920.1327344481340.6509654416960.03993689619870.47659079815310.9220867031103.0753078415.26139116212
103.709495149360.8939953344452.380417958541.214539839841.273948013985.01747746283-0.183017502603-0.662326819764-0.227649537603-0.139744781768-0.2326497169060.0310615532651-0.62973414767-0.20546857516-0.03034410115890.8698128302350.05321578110670.05864292173120.2755061475860.0787662795109-0.065145777519726.4795792364106.83845255916.0406683216
114.7292898633-1.202312881992.940056207376.0616036354-2.151825292233.45298704245-0.3010397192290.1086462377950.251030490224-0.06057097093890.2318483969140.0401503886569-0.1319904390330.720104316560.153073771270.7014544695860.1622199299010.04264925224410.401990134188-0.02141306715110.23667930399729.655900776107.3312523354.78366753286
122.49567099435-0.430610107057-0.7509492811433.5075819021-0.4911984065542.16650562547-0.5037365682530.302030384558-0.419125961406-0.6204799303920.285719363534-0.0955541989526-0.00835869784430.0833152822510.2914643663770.619361983005-0.0276584842470.1109043002180.3263492642030.01716623752230.26096717656427.890115583798.11163208038.08103106113
136.777200098560.5932339621011.263296501892.10440560361-0.7070872945663.36618179583-0.269184532572-0.317732875550.2061126697510.3631582986350.3363530743610.429430629114-0.3236161764190.330406503255-0.09102486204910.4791866671210.0448634001430.1131643303430.3351370415960.09308301370810.14713396192922.2561379954103.32868254415.808889516
143.448170819491.93973040332-0.5213731625086.87559325404-0.5011396956565.53361904922-0.00614216562030.1974592494330.587396585194-0.3657288410910.567081940051-0.0722781013795-0.5676072052120.142416770781-0.3490450791040.777549414792-0.057505748484-0.06294155239160.3624295568280.05422307905630.15766271537619.597155931115.0084956013.80716558872
152.098295555722.016117727440.1653468269094.94228293356-2.068062212492.450550161810.537756651987-0.0804664021511-0.07177083557670.611314582556-0.486788088959-0.615195762355-0.850155174434-0.3365646008950.04731662756040.6715567400440.145261504949-0.1363206245880.5438801447810.06075893884230.50677053160319.9788588652110.84575363113.320833484
161.402184117611.308637111191.229991295621.235474458011.056660484421.463771916350.106291970133-0.555504186742-0.4525027875050.4394857803570.303941253982-0.3943199713110.2415395946030.1172437106850.09514305258190.1707254341820.299262163381-0.5611389613060.3630288825110.3393634220690.25584281149331.769361162194.729028387421.2629835109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 6 )
2X-RAY DIFFRACTION2chain 'A' and (resid 7 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 95 )
7X-RAY DIFFRACTION7chain 'A' and (resid 96 through 114 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 24 )
9X-RAY DIFFRACTION9chain 'B' and (resid 25 through 32 )
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 51 )
11X-RAY DIFFRACTION11chain 'B' and (resid 52 through 68 )
12X-RAY DIFFRACTION12chain 'B' and (resid 69 through 91 )
13X-RAY DIFFRACTION13chain 'B' and (resid 92 through 99 )
14X-RAY DIFFRACTION14chain 'B' and (resid 100 through 109 )
15X-RAY DIFFRACTION15chain 'B' and (resid 110 through 119 )
16X-RAY DIFFRACTION16chain 'B' and (resid 120 through 129 )

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