PDB-8guo: Crystal structure of the nuclease domain of EsaD in complex with ...

ID or keywords:

Entry

Database: PDB / ID: 8guo

Title

Crystal structure of the nuclease domain of EsaD in complex with EsaG from Staphylococcus aureus

Components

Type VII secretion system protein EsaG
Type VII secretion system protein EssD

Keywords

TOXIN/ANTITOXIN / TOXIN ANTITOXIN / TOXIN / TOXIN-ANTITOXIN complex

Function / homology

Function and homology information

extracellular region / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.59395167886 Å

Authors

Zhang, Z.M. / Wang, Y.J.

Funding support

1items

Citation

Journal: Nat Commun / Year: 2022
Title: A toxin-deformation dependent inhibition mechanism in the T7SS toxin-antitoxin system of Gram-positive bacteria.
Authors: Wang, Y. / Zhou, Y. / Shi, C. / Liu, J. / Lv, G. / Huang, H. / Li, S. / Duan, L. / Zheng, X. / Liu, Y. / Zhou, H. / Wang, Y. / Li, Z. / Ding, K. / Sun, P. / Huang, Y. / Lu, X. / Zhang, Z.M.

History

Deposition	Sep 13, 2022	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Nov 9, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8guo.cif.gz	147.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8guo.ent.gz	95.9 KB	Display	PDB format
PDBx/mmJSON format	8guo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8guo_validation.pdf.gz	435 KB	Display	wwPDB validaton report
Full document	8guo_full_validation.pdf.gz	437.1 KB	Display
Data in XML	8guo_validation.xml.gz	12.3 KB	Display
Data in CIF	8guo_validation.cif.gz	16.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gu/8guo ftp://data.pdbj.org/pub/pdb/validation_reports/gu/8guo	HTTPS FTP

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Related structure data

Related structure data	8gunC 8gupC 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

Deposited unit

A: Type VII secretion system protein EsaG

B: Type VII secretion system protein EssD

38.8 kDa, 2 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)	111.776, 111.776, 171.228
Angle α, β, γ (deg.)	90.0, 90.0, 90.0
Int Tables number	97
Space group name H-M	I422
Space group name Hall	I42
Symmetry operation	#1: x,y,z #2: -y,x,z #3: y,-x,z #4: x,-y,-z #5: -x,y,-z #6: -x,-y,z #7: y,x,-z #8: -y,-x,-z #9: x+1/2,y+1/2,z+1/2 #10: -y+1/2,x+1/2,z+1/2 #11: y+1/2,-x+1/2,z+1/2 #12: x+1/2,-y+1/2,-z+1/2 #13: -x+1/2,y+1/2,-z+1/2 #14: -x+1/2,-y+1/2,z+1/2 #15: y+1/2,x+1/2,-z+1/2 #16: -y+1/2,-x+1/2,-z+1/2

#1: Protein	Type VII secretion system protein EsaG Mass: 19618.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Gene: essG, esaG, SAOUHSC_00269 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2G178
#2: Protein	Type VII secretion system protein EssD / Nuclease toxin EssD Mass: 19216.658 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Gene: essD, esaD, SAOUHSC_00268 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2G179
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.44 Å³/Da / Density % sol: 64.3 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris pH 8.5, 12% PEG6000, 0.15M NaCl, 10% Ethylene glycol, 0.5% Tacsimate pH 7.0, 1.0% PEG5000MME

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.97869 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: May 17, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97869 Å / Relative weight: 1
Reflection	Resolution: 2.59→50 Å / Num. obs: 16955 / % possible obs: 100 % / Redundancy: 20 % / B_iso Wilson estimate: 34 Å² / CC_1/2: 0.976 / Net I/σ(I): 31.2
Reflection shell	Resolution: 2.6→2.64 Å / Num. unique obs: 16953 / CC_1/2: 0.984

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692+SVN	refinement
HKL-3000		data reduction
HKL-2000		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.59395167886→23.1360929682 Å / SU ML: 0.275489545734 / Cross valid method: FREE R-VALUE / σ(F): 1.41322623495 / Phase error: 23.0841738868

	R_factor	Num. reflection	% reflection
R_free	0.22573768119	1706	10.0625221187 %
R_work	0.206017262792	15248	-
obs	0.208013796011	16954	98.7707544422 %

Solvent computation

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

Displacement parameters

B_iso mean: 34.2137578934 Å²

Refinement step

Cycle: LAST / Resolution: 2.59395167886→23.1360929682 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2103	0	0	121	2224

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00317111760284	2154
X-RAY DIFFRACTION	f_angle_d	0.734952939118	2906
X-RAY DIFFRACTION	f_chiral_restr	0.0296562483786	297
X-RAY DIFFRACTION	f_plane_restr	0.00314344347081	372
X-RAY DIFFRACTION	f_dihedral_angle_d	17.1004629862	803

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 (%)
2.594-2.6702	0.297693573464	127	0.238688691765	1230	X-RAY DIFFRACTION	97.7665706052
2.6702-2.7562	0.28829655119	150	0.245749035632	1259	X-RAY DIFFRACTION	100
2.7562-2.8546	0.290872685087	152	0.233432479959	1258	X-RAY DIFFRACTION	99.9291282778
2.8546-2.9686	0.259039497224	128	0.246063676092	1274	X-RAY DIFFRACTION	99.9287241625
2.9686-3.1034	0.276622583765	146	0.261322341124	1258	X-RAY DIFFRACTION	99.8577524893
3.1034-3.2666	0.25247122466	142	0.229494540817	1265	X-RAY DIFFRACTION	99.7165131113
3.2666-3.4707	0.236489984911	134	0.217638035109	1281	X-RAY DIFFRACTION	99.8588567396
3.4707-3.7376	0.234515274575	154	0.193648205492	1273	X-RAY DIFFRACTION	99.7902097902
3.7376-4.1119	0.223965127976	140	0.192114564146	1281	X-RAY DIFFRACTION	99.5795374912
4.1119-4.7025	0.141681837996	142	0.164608448524	1289	X-RAY DIFFRACTION	98.8942639945
4.7025-5.9083	0.187340107799	140	0.180871301291	1288	X-RAY DIFFRACTION	97.6076555024
5.9083-10	0.222484986802	151	0.199536541431	1292	X-RAY DIFFRACTION	93.0367504836

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	1.13152036983	-0.827398699301	-0.542171644867	1.3434683901	0.918874531597	2.8197612564	-0.165148925359	0.301278644	-0.154458633732	-0.0459106630404	-0.105800187291	0.21731193271	0.0137283975428	-0.273308506526	0.260426576914	0.281716758471	-0.0249606645954	0.073961117154	0.342699410903	-0.00625306958123	0.28451857233	153.261288006	141.367334804	189.096108731
2	1.62445098115	0.568686808397	-0.090352808614	2.40762207081	-0.663637949801	1.53670975763	-0.101682724882	0.124971773165	0.0964824985176	0.654181706232	0.0570398478289	0.181604943372	-0.200228767634	-0.132693474627	0.0154875599493	0.337158756571	0.00470051756173	0.0644666002355	0.262780725563	-0.0202456897928	0.273722401539	152.968896577	147.296969217	202.207977104
3	2.29384956315	-1.5541120909	-1.23057500084	2.08643023796	0.433136966596	1.92503644947	-0.352551225747	0.195243509775	-0.58542273877	0.341473527121	-0.117313393932	0.334220253613	0.634851571022	-0.29146973246	0.361289542809	0.304818678638	-0.0668363202303	0.0782155574731	0.296009478486	-0.0237698648462	0.318966928423	152.464270811	132.84504318	194.912519843
4	1.96607903706	-1.7807293038	0.424137508938	2.59156573621	-0.372314942396	1.26057627535	0.178948184818	0.270547822732	-0.0352696468746	-0.153586292775	-0.261333870414	0.0116220446039	0.184263855223	0.0251340020292	0.100351990323	0.328573211348	-0.0291264944364	0.0683492520392	0.251387130212	0.0164386494874	0.28310645284	162.251189782	136.245496305	188.060732114
5	6.57100799171	-2.04820596386	-0.281824475282	1.33287061693	0.5525824172	2.05662379175	-0.645725817253	0.886168372855	0.753640020933	0.617682530492	-0.000471995367589	-0.741252730668	-0.490267226296	0.139919737463	0.415016201515	0.431988280132	-0.0620615856287	-0.00245629751471	0.298880441834	0.0739034503525	0.213485949712	159.43144525	146.442884659	186.477184703
6	1.16664134584	-0.111735836415	0.266892128929	0.976279021185	0.241208461139	4.45548150884	-0.307787953795	-0.06939066919	-0.543102641818	-0.0225935426473	-0.307428374839	-0.25781074113	1.4308071705	0.446746865373	0.260835479256	0.409625503619	0.0329567643168	0.0799390833411	0.348119068303	0.0755844901566	0.429949178793	171.493271505	131.708350158	199.982477027
7	1.99271117685	-0.971292728191	0.386411187839	0.912953766525	-0.930255050972	3.09869193139	-0.193984718485	-0.161266691107	0.20594826722	-0.691422622268	-0.0267437407651	-0.530229472194	0.139363157208	0.105474089937	0.167439259577	0.357863932807	-0.0836917157831	0.0750978491309	0.335419662665	-0.000437050486622	0.408871015526	167.882144738	144.096083841	201.894952106
8	4.52714995534	-0.780028859298	4.95549867717	4.49119653753	-3.84334472842	7.50432140455	-0.762533226224	-0.775678092123	1.22816065915	0.702682987312	-0.421816052139	-0.27698126033	-1.19061554388	0.314432599546	1.00625636312	0.475496230723	-0.0438821878994	0.00865224696233	0.476812737161	-0.0372865545721	0.46222501112	168.844910234	151.18407635	206.858779476
9	3.57047757236	0.218756896416	-0.689521094035	2.16566097684	-0.79503734097	2.27330348488	0.125303583977	-0.284490161804	0.259945330085	0.190852777667	-0.344655394403	-0.396610436606	-0.206514566249	0.264090413026	0.346363564798	0.32463426245	-0.0276586391122	-0.0389963295459	0.447830768715	0.0757659468233	0.355389685912	177.116412458	141.14394221	205.274103677
10	4.08101433128	-1.86437621409	0.926053130839	1.43142608883	-0.727617984846	1.65246590921	-0.0368128278267	0.265601756162	0.170603968118	-0.0202227956668	-0.219582710502	-0.362990685321	0.228995345252	0.0166081562163	0.131089718312	0.383457174879	0.0430476501087	0.0913428927778	0.416669106327	-0.0193246126699	0.277573533315	167.925521739	138.417177166	177.049496475
11	2.59196449248	0.0298131120455	-1.69186070282	3.00377239482	0.276769620346	1.40895404098	-0.132240562145	0.580431940584	0.43571382399	-0.305580838689	-0.145193926063	-0.239580151593	-0.0213817858778	-0.100145834907	0.217302746827	0.350508296329	0.00712708205362	0.0813615030035	0.283127223812	-0.0448649229876	0.225480799267	159.689697701	142.614306427	184.039700707
12	2.59944797581	1.14033615083	-0.348170554221	2.00508395066	-0.431127157601	1.84039369011	-0.144180470159	-0.517980639714	-0.0299653301974	0.459404179684	0.182557792557	-0.282584859503	0.142343388301	0.973031681363	0.146468017107	0.42596725575	0.0221458838568	0.0449589229849	0.490836830077	0.122529922375	0.372974375894	164.875502823	134.422424134	215.305465253
13	2.09949866599	0.95069736374	0.338573073614	2.75722365493	2.13858426332	3.86681823409	-0.772341957268	0.30816033803	-0.16276273259	-0.677528474193	0.443469698695	0.389721410268	0.431323069314	0.130500315083	0.289508603871	0.649612408387	-0.00437631598603	0.121556263607	0.466444004473	0.135467528267	0.46507440212	150.021514109	123.983110586	207.417774006
14	2.59108798555	-0.585511886924	0.960860184278	3.37110342805	-0.315437086868	1.20417905313	0.155645312047	-0.230989475743	-0.131391130866	-0.151151767249	-0.423122739793	-0.490127036989	0.100956546237	-0.0910138225895	0.0421317153963	0.421632528073	0.00817543289926	0.120081929835	0.321752248411	0.0674157856523	0.294841018205	156.234843731	132.900755819	208.103385526

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 67 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 91 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 92 through 105 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 106 through 115 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 116 through 125 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 126 through 137 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 138 through 144 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 145 through 161 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 470 through 491 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 492 through 558 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 559 through 580 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 581 through 593 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 594 through 614 )

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