PDB-8gun: Crystal structure of mutant H528A of EsaD from Staphylococcus aureus

ID or keywords:

Entry

Database: PDB / ID: 8gun

Title

Crystal structure of mutant H528A of EsaD from Staphylococcus aureus

Components

Type VII secretion system protein EssD

Keywords

TOXIN

Function / homology

Pre-toxin TG domain / Pre-toxin TG / : / Type VII secretion system protein EssD-like / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / extracellular region / plasma membrane / Type VII secretion system protein EssD

Function and homology information

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.30001380765 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	8gun.cif.gz	180.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8gun.ent.gz	120 KB	Display	PDB format
PDBx/mmJSON format	8gun.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8gun_validation.pdf.gz	577.1 KB	Display	wwPDB validaton report
Full document	8gun_full_validation.pdf.gz	576.9 KB	Display
Data in XML	8gun_validation.xml.gz	13.9 KB	Display
Data in CIF	8gun_validation.cif.gz	18.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gu/8gun ftp://data.pdbj.org/pub/pdb/validation_reports/gu/8gun	HTTPS FTP

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Related structure data

Related structure data	8guoC 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 EssD

B: Type VII secretion system protein EssD

hetero molecules

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

1

A: Type VII secretion system protein EssD

hetero molecules

defined by author
Evidence: gel filtration
20.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Type VII secretion system protein EssD

hetero molecules

defined by author
20.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	106.548, 106.548, 151.062
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

Components on special symmetry positions

ID	Model	Components
1	1	A-820- HOH
2	1	A-832- HOH

#1: Protein	Type VII secretion system protein EssD / Nuclease toxin EssD Mass: 20443.982 Da / Num. of mol.: 2 / Mutation: H528A 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
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 52.92 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2M (CH3COO)2Mg, 20% PEG3350

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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: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Oct 7, 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: 2.25→95.9 Å / Num. obs: 35443 / % possible obs: 96 % / Redundancy: 10.8 % / B_iso Wilson estimate: 45.6 Å² / CC_1/2: 0.998 / Net I/σ(I): 17.6
Reflection shell	Resolution: 2.25→2.37 Å / Num. unique obs: 2713 / CC_1/2: 0.737

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.30001380765→87.0690961637 Å / SU ML: 0.310593382641 / Cross valid method: FREE R-VALUE / σ(F): 1.35591409123 / Phase error: 24.0208219094

	R_factor	Num. reflection	% reflection
R_free	0.232966712844	3527	9.95118923342 %
R_work	0.181167088404	31916	-
obs	0.186331060641	35443	95.8825916407 %

Solvent computation

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

Displacement parameters

B_iso mean: 58.002301635 Å²

Refinement step

Cycle: LAST / Resolution: 2.30001380765→87.0690961637 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2639	0	2	65	2706

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0026938288143	2694
X-RAY DIFFRACTION	f_angle_d	0.603935093871	3624
X-RAY DIFFRACTION	f_chiral_restr	0.0237569489304	376
X-RAY DIFFRACTION	f_plane_restr	0.00336477477239	473
X-RAY DIFFRACTION	f_dihedral_angle_d	13.4522919269	1012

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 (%)
2.31-2.3315	0.329024248134	146	0.263058286413	1345	X-RAY DIFFRACTION	100
2.3315-2.3648	0.32348706225	141	0.254831939136	1339	X-RAY DIFFRACTION	99.9324780554
2.3648-2.4001	0.357650390022	143	0.260486933764	1319	X-RAY DIFFRACTION	100
2.4001-2.4376	0.285343642595	145	0.252854089658	1325	X-RAY DIFFRACTION	99.5260663507
2.4376-2.4776	0.276612472588	150	0.246616549562	1354	X-RAY DIFFRACTION	99.800928998
2.4776-2.5203	0.264257960917	149	0.240141705544	1286	X-RAY DIFFRACTION	100
2.5203-2.5662	0.304679398962	145	0.251391773716	1364	X-RAY DIFFRACTION	100
2.5662-2.6155	0.266611982605	145	0.232279933399	1325	X-RAY DIFFRACTION	100
2.6155-2.6689	0.291830217685	124	0.223774297566	1114	X-RAY DIFFRACTION	94.5038167939
2.6689-2.727	0.298161436835	118	0.218532326666	1069	X-RAY DIFFRACTION	91.237509608
2.727-2.7904	0.269202646106	150	0.206034515672	1320	X-RAY DIFFRACTION	100
2.7904-2.8602	0.259094190369	134	0.197163913394	1326	X-RAY DIFFRACTION	100
2.8602-2.9375	0.275738348325	155	0.19404482411	1371	X-RAY DIFFRACTION	100
2.9375-3.024	0.268924689622	142	0.219088698087	1310	X-RAY DIFFRACTION	100
3.024-3.1216	0.233101336853	155	0.204912331647	1337	X-RAY DIFFRACTION	100
3.1216-3.2331	0.26838402989	148	0.203842745609	1345	X-RAY DIFFRACTION	100
3.2331-3.3626	0.235933445362	154	0.1829878996	1308	X-RAY DIFFRACTION	100
3.3626-3.5156	0.263615752379	139	0.193376314514	1132	X-RAY DIFFRACTION	87.0547945205
3.5156-3.701	0.25955596403	88	0.184542246021	869	X-RAY DIFFRACTION	64.2713230356
3.701-3.9329	0.1805404223	133	0.157113409006	1122	X-RAY DIFFRACTION	83.7783711615
3.9329-4.2365	0.212229876161	148	0.149508131022	1305	X-RAY DIFFRACTION	100
4.2365-4.6628	0.156029330001	158	0.134497688008	1303	X-RAY DIFFRACTION	99.7269624573
4.6628-5.3375	0.175376416088	147	0.152800524202	1363	X-RAY DIFFRACTION	100
5.3375-6.7243	0.244505823703	134	0.161109551812	1332	X-RAY DIFFRACTION	100
6.7243-10	0.23199215725	136	0.171534677894	1333	X-RAY DIFFRACTION	98.3266398929

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	4.58796548609	1.85995673155	-3.00919984185	4.54338234403	-3.72126769456	7.66923472468	-0.22294395177	-0.306951536892	-0.0829803804383	-0.292471275901	0.631270435421	-0.531969912565	0.0588576408808	-0.067070659361	-0.525733462838	0.663282301992	-0.301265203259	-0.0589883352895	1.27560325614	-0.0798599037399	0.716080984715	1.37730859656	40.5382247852	-9.42884104241
2	6.71896400418	0.538178667409	4.67044753534	4.61579498688	5.76696892299	9.67123106969	0.310181050095	-0.313137491829	0.0360843725247	-0.289389854819	-0.688575242019	0.123171223712	-1.88306235557	0.474432300558	-0.0431169217553	0.843386115542	-0.450883594829	-0.0836444823824	0.586734482807	0.173575700207	0.646091776831	-8.2787774113	50.2942986	-23.9195850161
3	3.29584821952	1.00892012788	-0.617589990933	2.86058837548	-0.326440839349	1.70665049335	-0.156146987009	-0.181760430947	0.0120360542082	-0.0736904982265	-0.0134988873558	-0.0203452501398	-1.10117015943	1.43438147892	-0.0357196347203	0.549530228597	-0.329160414278	-0.0917862443505	0.831711303025	0.119263976808	0.513265740773	-5.1893287207	43.1470571359	-18.141254998
4	1.13222377944	0.825242656858	-1.96492635687	3.69768423278	-2.05605444134	3.67805315395	-0.0466681586471	-0.0241914148481	0.0452664226898	0.367062159205	-0.0212514418768	0.102730447973	-0.831950786591	0.75079755607	0.091221519053	0.396968763476	-0.229417988262	0.0708095591705	0.711214766926	-0.0268014439764	0.53330923703	-11.5969199816	37.0456460395	-12.2011621241
5	4.87934913668	-5.05845216302	-2.60486021796	5.31917101704	3.26250529089	8.56711855927	0.563528971261	1.45211785521	0.0879934649207	-1.96231861041	-0.419046919112	0.421524141889	-1.31296567251	0.518328626372	-0.0550415176009	0.921760899006	-0.23057639961	-0.0795483790696	0.797317358537	0.0755265741554	0.614033245347	-13.7695988504	37.8323325132	-33.853747139
6	2.91164136767	1.65415803873	-0.38234407249	3.85677969572	1.23818183274	6.22150099014	-0.216234929561	0.378199052219	0.137693271488	-0.5513683506	-0.0331971848145	0.483696797562	-0.561265782229	0.302854159174	0.259298257402	0.382080064166	-0.131165692278	-0.0783728323152	0.46659579732	0.0766767432796	0.438383984514	-16.1491770934	35.4542955269	-23.6627257529
7	3.7559677104	2.34840746878	0.627709903865	4.84334198491	1.0139756907	5.9829952012	-0.386566703776	0.570367705837	-0.323574372443	-0.402877169332	0.131763085975	-0.0590826719799	0.542342938052	0.575830111292	0.302278376114	0.349343675123	-0.0685871393451	0.0832567029769	0.450103658461	-0.00715173287021	0.435346142222	-16.5719261282	24.8129643715	-25.9789707159
8	2.85151055704	0.192752821022	-3.48118520811	0.0540058278746	-0.376499390617	8.71033999952	0.0632018604643	-0.104108147878	0.168064455106	-0.0852979148027	-0.0207691855441	-0.1267694902	0.273096326631	0.393994728699	0.028954562158	0.496664449553	-0.111825463525	0.0490760493907	0.40466521215	0.0420991713203	0.527323145986	-18.3014227126	25.4208564985	-12.6984427156
9	5.70618620424	3.39031309216	-3.68799899889	3.54369772861	-2.35897014176	8.32626057328	-0.183596575952	-0.885621800823	-0.500551055319	0.0916818840549	-0.425040105122	-0.450424253695	0.451080295619	1.48497863658	0.629374231145	0.43648256391	-0.0828129765845	0.00757812658957	0.598651980176	0.130313054042	0.44280216099	-9.71137863294	30.7923111764	-8.79478789522
10	4.8317652344	0.940536618538	-1.25422864125	5.16584072403	1.70398164522	1.39375451306	-0.0401381019577	0.573968667928	-0.130700805996	-0.279085612189	0.121062639139	-0.18190764364	-0.323555452228	1.63586979174	-0.0777295350017	0.311555126672	-0.0779559789846	0.0474673875605	0.715494703727	0.0894346235789	0.454032845828	-4.82902935336	30.2200117867	-21.3879613802
11	7.31876943792	-0.214947906855	-4.0667025634	5.08539729855	-0.0161117692414	2.3287669154	-0.310098374524	-0.515128875285	-0.37298248757	0.37264117806	0.00817009004156	-0.249880035713	1.71322211891	0.901100232006	0.355104293466	0.482277365514	0.0521399700705	0.000963010216447	0.531949418812	-0.0076690945083	0.572831522416	-7.51485885559	23.5152585163	-13.0751601156
12	5.05213501332	1.16221717909	2.72259169841	5.96483217906	-0.000333863030557	2.91318105714	-0.407702866236	0.465298304467	0.223335237971	-0.35243377099	0.58581478312	0.312789688933	-0.183738652198	-0.16445496084	-0.239283160292	0.414988706482	0.00922606496626	-0.0121071661037	0.813360135837	0.0983785103397	0.535980101198	-54.5976064392	26.1842322262	-26.0788428103
13	7.32829708853	0.705633111638	-0.534722118586	4.75331039702	-0.432813034113	5.62400504512	-0.223662661485	-0.207636425915	0.990828470085	0.0802042689425	0.156480632186	0.0887317735009	-0.714122182632	-0.618807064876	0.0234934272225	0.511154447909	0.0871498928452	-0.0269159340815	0.61071728726	0.0316732289217	0.61555895041	-51.662728251	31.4448889479	-19.1967555727
14	5.31465146072	-0.289020934435	-0.158132856631	4.88958423172	3.1846036775	8.03987659451	-0.137432026258	-0.157134881701	0.57215921967	-0.187869501659	0.0524506252211	0.0382834062455	-0.865452274264	-0.766201188278	0.0768587737609	0.450479852304	-0.0113273042797	-0.000771737391664	0.446568413825	0.0425434825241	0.471298727632	-41.2745802735	29.0750766192	-13.8980581616
15	4.03385910359	0.95244948761	1.8199481924	1.23798654748	0.505605422219	2.94136305397	0.0657479661648	-0.259885821726	0.0575740210457	0.0211235890599	-0.189753917677	-0.160161877699	-0.404740321361	-0.0868975010955	-0.0220489949908	0.475982676469	-0.108592885512	0.0858215019833	0.444992443024	0.0576561378241	0.501691437802	-35.1326258412	27.2158472031	-13.3026827484
16	2.96024018639	1.04857521479	0.190010233265	0.710740094375	1.27364663015	4.56515594451	0.105415354844	-0.0442271419351	-0.436099478784	0.11501736236	0.206466434122	-0.303751528097	0.29194900698	0.089962812894	-0.219696110505	0.435582963212	-0.128585266727	0.0414027398486	0.488443612864	0.0290711916301	0.586387765993	-29.8515475331	20.2120935534	-20.429350208
17	6.85546390308	0.714032957561	1.34303185139	5.64908748475	1.66342703495	5.80418035967	0.0851725141786	0.389099836768	-1.34977315788	-0.136772897356	0.0420569996152	0.0757381425612	-0.102523387435	-0.693857580934	0.0574570359063	0.409469042781	-0.117107105234	0.0177935416737	0.445478113218	0.0379049857984	0.539671504186	-39.4426691999	17.9459097496	-24.9246636068
18	6.65201228184	-1.15932459059	-1.77930090983	4.54815090869	0.689479378708	3.75946850779	0.224472802786	-0.313438907743	-0.698233166101	0.508612134135	-0.535447661514	0.510263529267	0.10899878048	-1.57100148541	0.423475403191	0.355516735556	-0.0992302863778	-0.00805752358633	0.737217557561	0.153209163284	0.499020088062	-44.7727108161	19.7971235569	-13.0577815524
19	6.87045491623	-0.262690518736	-2.92407208782	6.36348375081	4.21422931735	3.85640184631	-0.434958645423	-0.217258044198	-0.997638476893	-0.300068032898	-0.212927800198	0.529713597945	0.406047456233	0.171880741493	0.495850115155	0.559629059883	-0.163382494269	-0.0750336098385	0.50521452186	0.145607660346	0.605173632191	-37.8885638973	13.41022852	-17.2953548405

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 444 through 453 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 454 through 471 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 472 through 491 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 492 through 509 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 510 through 519 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 520 through 542 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 543 through 558 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 559 through 572 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 573 through 585 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 586 through 602 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 603 through 614 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 445 through 461 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 462 through 491 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 492 through 528 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 529 through 558 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 559 through 572 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 573 through 585 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 586 through 602 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 603 through 614 )

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