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

ID or keywords:

Entry

Database: PDB / ID: 9g4g

Title

Staphylococcus aureus MazF in complex with Nanobody 9

Components

Endoribonuclease MazF
Nanobody 9

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: 2.89572919242 Å

Authors

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-Kalinsec, M. / Zorzini, V. / Haesaerts, S. / De Bruyn, P. / Loris, R.

History

Deposition	Jul 15, 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	9g4g.cif.gz	131.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9g4g.ent.gz	85.7 KB	Display	PDB format
PDBx/mmJSON format	9g4g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9g4g_validation.pdf.gz	447.3 KB	Display	wwPDB validaton report
Full document	9g4g_full_validation.pdf.gz	450.1 KB	Display
Data in XML	9g4g_validation.xml.gz	11.9 KB	Display
Data in CIF	9g4g_validation.cif.gz	15.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g4/9g4g ftp://data.pdbj.org/pub/pdb/validation_reports/g4/9g4g	HTTPS FTP

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Related structure data

Related structure data	9g1yC 9g2gC 9g48C 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: Nanobody 9

hetero molecules

29.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Endoribonuclease MazF

B: Nanobody 9

hetero molecules

A: Endoribonuclease MazF

B: Nanobody 9

hetero molecules

defined by author&software
Evidence: gel filtration
59.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
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

#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 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: 2.78 Å³/Da / Density % sol: 55.76 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.978 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 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: 2.89572919242→46.0840534125 Å / Num. obs: 7201 / % possible obs: 93.5 % / Redundancy: 4.8 % / B_iso Wilson estimate: 43.425238765 Å² / CC_1/2: 0.99 / Net I/σ(I): 9.51
Reflection shell	Resolution: 2.89572919242→3.07 Å / Mean I/σ(I) obs: 2.65 / Num. unique obs: 1195 / CC_1/2: 0.842

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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: 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

	R_factor	Num. reflection	% reflection
R_free	0.303201178834	360	5.00556173526 %
R_work	0.252761150504	6832	-
obs	0.255352559346	7192	93.4511434511 %

Solvent computation

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

Displacement parameters

B_iso mean: 50.9482501898 Å²

Refinement step

Cycle: LAST / Resolution: 2.89572919242→46.0840534125 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1822	0	5	74	1901

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00216512316656	1858
X-RAY DIFFRACTION	f_angle_d	0.570554595903	2520
X-RAY DIFFRACTION	f_chiral_restr	0.0439709526599	286
X-RAY DIFFRACTION	f_plane_restr	0.0037171493906	326
X-RAY DIFFRACTION	f_dihedral_angle_d	11.4061975687	1124

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 (%)
2.8958-3.3146	0.395602532407	122	0.330019279041	2318	X-RAY DIFFRACTION	97.1724412585
3.3146-4.1757	0.359122436199	114	0.275096939273	2173	X-RAY DIFFRACTION	90.0748326113
4.1757-46.0840534125	0.229269114361	124	0.203107816388	2341	X-RAY DIFFRACTION	93.1947069943

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	2.80068278448	1.86163948893	0.738387873378	2.24400007318	1.66489412666	1.95821238468	0.188904877638	-0.321805729758	0.519747423404	1.12692691562	-0.394897200756	0.37848442145	-1.20781610342	-0.81802179215	0.245107685875	0.973661957618	0.156823988183	4.01659820895E-5	0.55859655638	-0.111686199112	0.309783714189	16.9902973532	144.542315411	12.5126724083
2	1.53184076912	-1.84339559581	2.3020482493	3.1425270143	-1.3555269635	5.68650823712	-0.407197765316	0.245145341974	0.0331035005471	-0.330041582601	0.857839161959	0.0835634714232	-0.921979539745	-0.691668830911	-0.147312501626	1.31773190245	-0.268782156374	0.177524399252	0.704343600936	0.0919585656827	0.126961840075	8.55053886674	138.189164495	13.8255333268
3	6.03586733034	5.29302211163	6.10410119772	4.72160657096	5.71778937837	8.39567324906	1.14082059816	0.386298956128	-0.693823221292	1.2817974568	-0.458553718616	-0.144075962648	0.401328025942	0.701037105425	-0.637024619693	1.05531829087	-0.107186603948	0.0650981681594	1.23205185685	0.0985708919295	1.05649564869	2.03066041267	129.02628207	4.40066061258
4	5.5813450441	3.93360353573	-3.64973699221	7.53031870388	-4.30922319654	7.28297811327	0.251622516026	0.284964648306	0.135591719291	0.5672024317	0.284437910469	0.49357529834	0.26069719001	0.0676092057366	-0.0833860546872	0.626039345324	-0.0819308221862	-0.0839591323355	0.41490792747	-0.121321802458	0.231876435106	12.5645107466	136.542287183	9.42862592289
5	1.82088138746	-1.19268801702	0.0526878782045	6.96154608583	0.6277697774	1.81418827767	0.107534580045	0.139422233371	-0.229510088673	0.343760140344	0.11550806919	0.51247084875	-0.278146811027	-0.155245917689	-0.120895146203	0.594344257839	0.0296685561365	0.00926981886902	0.302627947478	-0.0383642930076	0.197308271852	15.0552395946	134.329245836	7.69248405277
6	3.01424728672	0.474209827472	-0.666079375293	2.78168693679	-1.14824956353	2.27965188754	0.126701822133	-0.462896126461	0.369847170053	0.701803121763	-0.282806634868	0.389540589566	-0.0327747852193	-0.332824521818	0.191903744921	0.849794503437	-0.0538032194576	-0.00809693123582	0.35631959394	-0.0545155771558	0.362683181951	13.107156478	132.942584835	14.0135895419
7	3.9751947208	-1.84613532783	1.74792302383	3.02014249697	-1.59119532885	5.75611311076	0.0924776939489	-0.493809526586	0.455074539257	0.706317271815	-0.209336258342	-0.654306835095	-0.188629945545	0.434812429513	0.0235023982348	0.618595242104	-0.0487390254262	-0.0193766154982	0.370510036648	-0.0452828842316	0.342848794828	25.9240478113	130.470212151	6.34682380674
8	9.5596045397	-2.09026185562	2.42524392577	2.84668731745	-0.45777236489	5.93542147756	0.060292000897	0.22197553379	-0.927377546292	-0.595980459066	-0.0717561814579	0.489522883923	1.34295638277	-0.0154424508446	-0.0015052541479	0.741628963494	-0.00600637514585	-0.0850359620038	0.331998122626	-0.0390551584886	0.427668183701	25.0503000528	94.7524832149	13.3854715629
9	1.20828685542	1.38577184379	-1.0812114108	2.89255172535	-2.58033515598	3.93923368595	-0.141118174742	0.663585770236	0.104665677799	-0.582906479873	-0.154619642357	0.11290666917	0.0673625864406	-0.440591313072	0.188868666425	0.968503829729	-0.268548250092	0.132734448134	0.650965441696	0.0399368961987	0.476590798153	10.9220867031	103.075307841	5.26139116212
10	3.70949514936	0.893995334445	2.38041795854	1.21453983984	1.27394801398	5.01747746283	-0.183017502603	-0.662326819764	-0.227649537603	-0.139744781768	-0.232649716906	0.0310615532651	-0.62973414767	-0.20546857516	-0.0303441011589	0.869812830235	0.0532157811067	0.0586429217312	0.275506147586	0.0787662795109	-0.0651457775197	26.4795792364	106.838452559	16.0406683216
11	4.7292898633	-1.20231288199	2.94005620737	6.0616036354	-2.15182529223	3.45298704245	-0.301039719229	0.108646237795	0.251030490224	-0.0605709709389	0.231848396914	0.0401503886569	-0.131990439033	0.72010431656	0.15307377127	0.701454469586	0.162219929901	0.0426492522441	0.401990134188	-0.0214130671511	0.236679303997	29.655900776	107.331252335	4.78366753286
12	2.49567099435	-0.430610107057	-0.750949281143	3.5075819021	-0.491198406554	2.16650562547	-0.503736568253	0.302030384558	-0.419125961406	-0.620479930392	0.285719363534	-0.0955541989526	-0.0083586978443	0.083315282251	0.291464366377	0.619361983005	-0.027658484247	0.110904300218	0.326349264203	0.0171662375223	0.260967176564	27.8901155837	98.1116320803	8.08103106113
13	6.77720009856	0.593233962101	1.26329650189	2.10440560361	-0.707087294566	3.36618179583	-0.269184532572	-0.31773287555	0.206112669751	0.363158298635	0.336353074361	0.429430629114	-0.323616176419	0.330406503255	-0.0910248620491	0.479186667121	0.044863400143	0.113164330343	0.335137041596	0.0930830137081	0.147133961929	22.2561379954	103.328682544	15.808889516
14	3.44817081949	1.93973040332	-0.521373162508	6.87559325404	-0.501139695656	5.53361904922	-0.0061421656203	0.197459249433	0.587396585194	-0.365728841091	0.567081940051	-0.0722781013795	-0.567607205212	0.142416770781	-0.349045079104	0.777549414792	-0.057505748484	-0.0629415523916	0.362429556828	0.0542230790563	0.157662715376	19.597155931	115.008495601	3.80716558872
15	2.09829555572	2.01611772744	0.165346826909	4.94228293356	-2.06806221249	2.45055016181	0.537756651987	-0.0804664021511	-0.0717708355767	0.611314582556	-0.486788088959	-0.615195762355	-0.850155174434	-0.336564600895	0.0473166275604	0.671556740044	0.145261504949	-0.136320624588	0.543880144781	0.0607589388423	0.506770531603	19.9788588652	110.845753631	13.320833484
16	1.40218411761	1.30863711119	1.22999129562	1.23547445801	1.05666048442	1.46377191635	0.106291970133	-0.555504186742	-0.452502787505	0.439485780357	0.303941253982	-0.394319971311	0.241539594603	0.117243710685	0.0951430525819	0.170725434182	0.299262163381	-0.561138961306	0.363028882511	0.339363422069	0.255842811493	31.7693611621	94.7290283874	21.2629835109

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 6 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 7 through 11 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 12 through 22 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 23 through 31 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 32 through 57 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 58 through 95 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 96 through 114 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 24 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 25 through 32 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 33 through 51 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 52 through 68 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 69 through 91 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 92 through 99 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 100 through 109 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 110 through 119 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 120 through 129 )

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