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

ID or keywords:

Entry

Database: PDB / ID: 9g2g

Title

Staphylococcus aureus MazF in complex with nanobody 5

Components

Endoribonuclease MazF
Nanobody 5

Keywords

TOXIN / 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

Biological species

Staphylococcus aureus (bacteria)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.80048236056 Å

Authors

Prolic-Kalinsek, M. / Zorzini, V. / Haesaerts, S. / Loris, R.

Funding support

Belgium, 1items

Citation

Journal: 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

Deposition	Jul 10, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 24, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9g2g.cif.gz	248 KB	Display	PDBx/mmCIF format
PDB format	pdb9g2g.ent.gz	164.5 KB	Display	PDB format
PDBx/mmJSON format	9g2g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9g2g_validation.pdf.gz	468.4 KB	Display	wwPDB validaton report
Full document	9g2g_full_validation.pdf.gz	473.6 KB	Display
Data in XML	9g2g_validation.xml.gz	22.5 KB	Display
Data in CIF	9g2g_validation.cif.gz	32.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g2/9g2g ftp://data.pdbj.org/pub/pdb/validation_reports/g2/9g2g	HTTPS FTP

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Related structure data

Related structure data	9g1yC 9g48C 9g4gC 9g5lC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Endoribonuclease MazF

B: Endoribonuclease MazF

C: Nanobody 5

D: Nanobody 5

hetero molecules

58.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

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 number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#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 interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 46.94 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 1.80048236056→46.9961366314 Å / Num. obs: 34576 / % possible obs: 78.8 % / Redundancy: 2.65 % / B_iso Wilson estimate: 23.6616470756 Å² / CC_1/2: 0.998 / Net I/σ(I): 13.55
Reflection shell	Resolution: 1.80048236056→1.91 Å / Mean I/σ(I) obs: 1.78 / Num. unique obs: 2227 / CC_1/2: 0.917 / % possible all: 34.4

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.243854432982	1596	4.94960458986 %
R_work	0.195452200843	30649	-
obs	0.197811004035	32245	73.7062265704 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 35.5688336135 Å²

Refinement step

Cycle: LAST / Resolution: 1.80048236056→46.9961366314 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3540	0	8	304	3852

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00443883729132	3723
X-RAY DIFFRACTION	f_angle_d	0.745453338116	5080
X-RAY DIFFRACTION	f_chiral_restr	0.0520552466107	571
X-RAY DIFFRACTION	f_plane_restr	0.00435837058	659
X-RAY DIFFRACTION	f_dihedral_angle_d	14.6007488078	2251

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8005-1.8586	0.343070169533	29	0.335308620119	744	X-RAY DIFFRACTION	19.325
1.8586-1.925	0.402408291016	58	0.290944860505	1070	X-RAY DIFFRACTION	28.5497342445
1.925-2.0021	0.287445532889	95	0.26174681231	1515	X-RAY DIFFRACTION	40.6873894364
2.0021-2.0932	0.304598159544	109	0.253398979803	2384	X-RAY DIFFRACTION	62.3717788341
2.0932-2.2036	0.28698071677	150	0.237922718545	3172	X-RAY DIFFRACTION	82.7397260274
2.2036-2.3416	0.277546865935	193	0.230414462123	3409	X-RAY DIFFRACTION	91.5607524148
2.3416-2.5224	0.294685550339	192	0.227786707693	3649	X-RAY DIFFRACTION	96.7019133938
2.5224-2.7762	0.268605647114	208	0.225881556041	3646	X-RAY DIFFRACTION	97.2495584153
2.7762-3.1779	0.273205347644	210	0.212808950263	3705	X-RAY DIFFRACTION	97.4365355898
3.1779-4.0035	0.220964048093	177	0.170198471837	3659	X-RAY DIFFRACTION	97.1631205674
4.0035-46.9961366314	0.174782776025	175	0.145861649906	3696	X-RAY DIFFRACTION	97.3346743777

Refinement TLS params.

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

ID	L11 (°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)
1	2.14693308959	-0.163514272534	0.140376899261	6.95471894283	0.544025515311	6.7306541672	-0.320787898791	-0.647739554132	-0.201133902303	0.108925781066	0.301985510973	-0.905257709968	0.670284068472	0.932094075089	0.0132967815418	0.342573313335	0.100199062384	-0.0303121167353	0.290689873175	0.00750339387304	0.316245356221	0.792382284112	-14.149828304	2.399250187
2	9.4331028549	4.79029836107	5.61506379254	5.70885195797	-0.396022117624	6.5601111826	0.145409494017	0.801265106699	0.0555374731309	-1.02274730976	0.229447314119	-2.63110243844	-0.12422150626	2.73490501864	-0.328802148315	0.633931659187	-0.0970147028651	0.347417827841	0.698448492165	-0.166931595189	1.15833495086	6.99504763899	2.33549975521	-1.79519419489
3	1.61328593222	-0.867568118974	-0.126220599671	1.38483335825	0.439149277389	1.87585919436	-0.165121293074	-0.454666562302	-0.0651934300735	0.369374059846	0.37094760493	-0.079626162744	0.240060177226	0.100110482291	-0.140178410547	0.172004381738	-0.00128821187423	-0.0135313934405	0.180055224207	0.0462785407674	0.135546455377	-6.96608729804	-7.90107030181	2.96751270128
4	2.70507768718	-1.55155262855	-0.572570018809	1.17719086506	1.04397248927	2.29877298838	-0.0792425331958	-0.69100041176	-0.0328657235604	0.296614117658	0.439246669409	-0.265263416704	0.00294511237641	0.468437636023	-0.262578336837	0.174788180427	0.0147864838309	-0.0373867274928	0.282944304721	-0.00501781802406	0.221372714411	-2.99066283185	-7.06626519532	4.50327807199
5	0.866831108483	0.458808983455	-0.512701742406	3.2673258442	-2.15804083781	4.87502966754	-0.00225117151203	-0.455784982662	-0.561530809828	0.331264284081	-0.118512952899	0.0419642933353	0.554592298793	-0.0480177155574	-0.182789251056	0.229772112001	-0.0821954814346	0.121831511892	0.241895101326	0.237292792404	0.296308944752	-17.4406206304	-11.7157625635	1.03814739652
6	4.4406470392	0.293554156552	-0.0505723359348	4.77566035187	-0.328163935808	3.76196352243	0.130099802774	0.385181333298	0.86189797398	-0.42308047657	-0.0501300435893	0.0589365405245	-0.8085636338	-0.0872991333568	-0.00152993082035	0.299598441962	0.0378164493222	0.0282744923386	0.211215530759	0.0665418669863	0.233607984844	-19.1280807097	5.74574509627	-17.3693645847
7	6.53772224272	-6.4651406008	3.29468038558	9.9061277707	-0.601349202117	3.66953071951	0.0362595232973	-1.46231400191	1.67017763555	1.02236808345	-0.591381059219	-2.81694747328	-0.638628023236	1.95565233857	0.50911047264	0.356528535478	-0.230332751733	-0.00397006927892	1.01902161293	-0.0485617766112	0.893782681809	-0.80365104029	3.93722044087	-14.4470816957
8	1.25527944106	0.230334599682	-1.21214770593	3.7225031185	-0.88163070294	4.0322970665	0.00886199066197	0.0656953868613	0.0206124713699	-0.426127596439	0.0226621364392	-0.256663259666	-0.31607964481	0.291633974718	0.418982900981	0.164227096264	-0.177699313402	0.0837181558282	0.0947689822963	0.0870375604939	0.0734701979553	-12.8992067901	-1.01287883275	-15.5416668558
9	1.86415497639	-0.883747826719	-0.495820540972	1.80849026265	0.385260454646	1.35585522607	0.236501800918	0.0135205999158	0.128841822264	0.0280142706886	-0.151596822466	-0.0910282181394	-0.065535834252	-0.108267381015	0.0347493429205	0.0531207253893	-0.0785933236665	0.08674568104	0.130321146018	0.0712959150934	0.0517128177297	-16.7623988031	1.53399999015	-10.221598664
10	3.7334834199	0.373419348367	-3.4175503434	8.33928522996	-6.35110699106	8.66988099766	0.421018301084	0.679030009221	-0.255219593321	-0.383234325316	-0.484815735229	0.0141084013278	0.0391003222937	0.159249376158	0.0313668705258	0.190739411054	0.0317029687922	-0.0230483415267	0.25352917544	-0.0434869104335	0.128904391583	-4.81520825293	-13.9405825313	-23.1320111518
11	2.26418747456	-1.68979059773	3.10347802608	2.13654176111	-2.21411001072	4.27501682724	0.468898388815	0.766553106353	0.0822043478669	-0.621311797478	-0.447493923506	-0.080071443282	-0.225397634603	-0.104706851828	-0.0513468099959	0.352742453035	0.190176541105	0.00395416157567	0.444802568339	0.00629459072763	0.14405688019	-13.0527418388	-7.49557265865	-28.396225665
12	0.888990271112	-1.5258912894	0.163953518099	3.73888284035	0.726506315897	0.934677166025	0.145279500758	0.120346792495	0.348558162744	-0.105078009706	-0.138533732777	-0.45008101934	-0.327089360436	0.367511411555	-0.0540769071223	0.127714194138	-0.0916024728179	0.0537632452668	0.196543317524	0.0112568324807	0.22041079582	-8.70674496266	-1.16779449909	-13.3281632609
13	5.27450608133	2.30387950733	2.9384529179	9.48777699996	3.53673488902	6.2305386879	0.0454708682398	0.937168775587	0.377837297637	-0.757652331654	-0.0567766282368	-0.0120403928126	-0.732351697485	0.144488172344	0.0381753748581	0.25581479774	0.0563271232898	0.0285926946702	0.261332234379	0.0804785079993	0.143010815724	-17.7163303591	1.85816025563	-21.8632421142
14	4.38851457635	-1.1445498811	1.95486375763	1.69587655647	-0.678914429132	6.03899045749	0.13971834792	0.119863908652	-0.467744370283	-0.015312570518	-0.117142399269	0.591008553541	0.44354431103	-0.628598387631	-0.0257888361653	0.202599692865	-0.122328315771	-0.0251902896245	0.154809320102	-0.0947330667252	0.373775157706	-17.2630428069	-14.4780845079	-13.1987273406
15	2.87715446191	-0.930668977143	-0.862777771581	1.88925922069	0.903750934318	0.644276897224	0.534329144939	0.905845213904	-0.200131447449	-0.69691271927	-0.366960868365	-0.158258749979	-0.0673324811531	-0.275561342592	-0.102751312788	0.631432793368	0.379570134569	-0.174273491141	0.637684252496	-0.202848747302	0.422387943526	13.785658338	-36.0034784135	-25.4396234236
16	4.36313155767	0.879055088318	0.967301827372	9.33375874592	-1.30166950145	3.33846234508	0.413130696612	0.966438716135	-0.109329686199	-0.270250095683	-0.106130560463	-0.653211149595	0.431543511972	0.668344055386	-0.141916967723	0.279955356783	0.188912190378	-0.0739513730509	0.466988014051	-0.0432091985299	0.298315657878	8.15775076245	-23.0892561536	-25.2466366643
17	4.02692522743	0.234516491019	-0.285865403268	3.16300282093	0.807589667283	5.20640473113	0.210524820132	0.461871835069	-0.57307002211	-0.0101840236701	0.107101762806	0.468016333787	0.595472460881	-0.0622582336632	-0.285896650998	0.269928563741	0.0366299166116	-0.111960702666	0.234987830492	-0.0023760844243	0.300427735631	3.87363676414	-29.5313393848	-15.9914288634
18	0.150469143666	-0.484005338217	0.635082349589	5.72722548952	-5.66420751642	5.82226704686	0.0517974923818	0.492752119447	0.0615258595831	-0.137614568377	-0.551281130378	-0.957411463385	-0.17186469195	0.802492731473	0.55961253636	0.3654383203	0.137669738406	0.00335716447436	0.508003495889	-0.00626683125108	0.447934781372	16.4430945618	-24.470457028	-21.9943042501
19	3.10072809436	-1.01978143563	1.43601250943	2.20755837414	1.58346816471	2.92168522307	0.634891516908	0.47886668619	-0.648873978309	-0.219193125216	-0.190599708901	0.0798722581063	0.542531706125	-0.17588178604	-0.303072206882	0.462632566512	0.148550967665	-0.262707921744	0.354492968136	-0.130416156506	0.554020577335	11.6813743053	-36.9350648359	-18.7272940456
20	1.05373604413	-1.52870629274	-0.690564916272	3.98234731919	0.412257084361	0.667967953007	0.636675544486	0.582627038984	-0.502970374997	-0.417711543337	-0.276412793144	0.0897198003781	0.527852311706	0.126183012166	-0.0553851258245	0.374993931089	0.134278372467	-0.193648747207	0.327547393049	-0.111571622641	0.353235508414	3.44751752794	-27.0162941993	-24.4353973834
21	1.75694175102	0.728106318483	1.06819733635	0.367243061622	0.848587738915	3.15443817754	-0.173946838533	-0.400354924207	0.177313214704	0.30047126977	0.193013538071	-0.231615897878	0.312277152045	0.143118063598	-0.39821467014	0.445524252779	0.238912241354	-0.223259402146	0.642486800683	-0.364859651214	0.450987622702	-23.0835272452	18.2245485742	17.975650664
22	0.505083482133	-1.06546005938	1.19049235452	2.34868986302	-2.01580973754	5.19635395845	-0.0801332461843	-0.308908844327	0.665440840529	0.241077018225	0.563645826894	-0.582778560266	-0.389194631017	-0.265573296035	-0.187742089234	0.349651093766	0.149467611794	-0.0488344380274	0.301866070744	-0.15705489018	0.394697693704	-37.0877410066	23.7795786897	9.28227093928
23	4.08989064453	1.34042138697	1.61550344941	6.73267770403	1.55669920392	1.86090391096	-0.130986325602	-0.289621563917	0.306144981928	0.126443753734	0.22664393691	-0.62459908704	-0.46046822907	0.413102624783	-0.226491169422	0.449626262811	-0.118703251796	-0.0233651797282	0.740646350048	-0.486309082995	0.926896844921	-15.6129543593	19.2898929907	10.2377703646
24	4.00437841137	2.0229960566	-4.82086509225	3.60285597856	-2.06253920036	5.86009997132	-0.380945907772	-0.214328403047	-0.127262733353	0.249344960034	0.350556919159	-0.125391392499	0.0541264973467	-0.288344950173	0.00828208467508	0.184949283213	0.0663499416184	0.0144929943442	0.259728105165	0.0346063107641	0.138373571305	-32.2722693081	9.8858097041	8.58332835306
25	1.37359953602	-1.23309480969	-1.79279537919	2.74998959319	-0.703716710832	5.6088396551	-0.126401906499	-0.105133880819	0.521435386626	0.0581127823576	0.302944728088	-0.234695445061	-0.292258923526	-0.255414771858	-0.0995752286953	0.184928841107	-0.0132634811549	-0.0455820505073	0.161546737669	-0.0250677350571	0.215647124321	-30.601256022	17.2197378825	3.86314648375
26	3.1916607293	-2.19319277394	-1.74260900489	2.74988609701	0.942731138897	1.12929091134	-0.32195885955	-0.63673937998	0.349636663086	0.176847325079	0.459645060738	-0.162026004042	-0.171095128203	-0.0936645495553	-0.155724605153	0.207272510643	0.107763537894	0.000763528244864	0.365733588477	-0.000700254943586	0.140193035161	-26.0971582519	10.9023055486	9.92716506978

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 11 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 22 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 23 through 66 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 67 through 95 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 96 through 114 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid -4 through 11 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 12 through 22 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 23 through 31 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 32 through 47 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 48 through 57 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 58 through 71 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 72 through 86 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 87 through 95 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 96 through 114 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 3 through 25 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 26 through 40 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 41 through 68 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 69 through 78 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 79 through 92 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 93 through 125 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 2 through 8 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 9 through 25 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 26 through 33 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 34 through 52 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 53 through 100 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 101 through 125 )

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