PDB-8gup: Crystal structure of EsaG from Staphylococcus aureus

ID or keywords:

Entry

Database: PDB / ID: 8gup

Title

Crystal structure of EsaG from Staphylococcus aureus

Components

Type VII secretion system protein EsaG

Keywords

ANTITOXIN

Function / homology

Immunity protein YezG-like / Immunity protein YezG-like superfamily / Immunity protein YezG-like / cytoplasm / CITRIC ACID / Type VII secretion system protein EsaG

Function and homology information

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.29872480327 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	May 29, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8gup.cif.gz	181.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8gup.ent.gz	121.5 KB	Display	PDB format
PDBx/mmJSON format	8gup.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8gup_validation.pdf.gz	903.3 KB	Display	wwPDB validaton report
Full document	8gup_full_validation.pdf.gz	906.4 KB	Display
Data in XML	8gup_validation.xml.gz	15.4 KB	Display
Data in CIF	8gup_validation.cif.gz	20.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gu/8gup ftp://data.pdbj.org/pub/pdb/validation_reports/gu/8gup	HTTPS FTP

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Related structure data

Related structure data	8gunC 8guoC 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 EsaG

hetero molecules

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

1

A: Type VII secretion system protein EsaG

hetero molecules

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

2

B: Type VII secretion system protein EsaG

hetero molecules

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

Unit cell

Length a, b, c (Å)	90.674, 62.106, 82.811
Angle α, β, γ (deg.)	90.0, 117.49, 90.0
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: Protein	Type VII secretion system protein EsaG Mass: 19618.732 Da / Num. of mol.: 2 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: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.64 Å³/Da / Density % sol: 53.33 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1M sodium phosphate/citric acid (pH4.2), 10% 3350 0.3M NaCl

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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 PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97869 Å / Relative weight: 1
Reflection	Resolution: 2.29→50 Å / Num. obs: 35477 / % possible obs: 100 % / Redundancy: 7.7 % / B_iso Wilson estimate: 51 Å² / CC_1/2: 1 / Net I/σ(I): 13.5
Reflection shell	Resolution: 2.3→2.38 Å / Num. unique obs: 35477 / CC_1/2: 0.925

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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:

SAD / Resolution: 2.29872480327→49.1580872655 Å / SU ML: 0.289900136936 / Cross valid method: FREE R-VALUE / σ(F): 1.40090161041 / Phase error: 27.7478888065

	R_factor	Num. reflection	% reflection
R_free	0.253417813767	3537	9.97096383165 %
R_work	0.216082256759	31936	-
obs	0.219855608258	35473	99.6040882799 %

Solvent computation

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

Displacement parameters

B_iso mean: 51.9514506641 Å²

Refinement step

Cycle: LAST / Resolution: 2.29872480327→49.1580872655 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2702	0	26	114	2842

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00260454343395	2798
X-RAY DIFFRACTION	f_angle_d	0.575777669348	3789
X-RAY DIFFRACTION	f_chiral_restr	0.0222666011438	382
X-RAY DIFFRACTION	f_plane_restr	0.00272122114418	489
X-RAY DIFFRACTION	f_dihedral_angle_d	18.1273486981	1025

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 (%)
2.3-2.3302	0.29749932458	131	0.270252528571	1161	X-RAY DIFFRACTION	93.2178932179
2.3302-2.3635	0.27746568137	139	0.249558957474	1296	X-RAY DIFFRACTION	99.930362117
2.3635-2.3988	0.325118235741	141	0.268684704508	1267	X-RAY DIFFRACTION	99.9290276792
2.3988-2.4363	0.286862560881	140	0.271219484153	1254	X-RAY DIFFRACTION	99.9283154122
2.4363-2.4762	0.315366246024	146	0.266091270584	1314	X-RAY DIFFRACTION	99.9315537303
2.4762-2.5189	0.299297738291	144	0.262799268981	1292	X-RAY DIFFRACTION	100
2.5189-2.5647	0.337574699333	137	0.259474223108	1237	X-RAY DIFFRACTION	100
2.5647-2.614	0.322808778255	145	0.283870895532	1311	X-RAY DIFFRACTION	100
2.614-2.6674	0.388002210976	141	0.271379830741	1276	X-RAY DIFFRACTION	100
2.6674-2.7254	0.298899743237	144	0.27120995058	1300	X-RAY DIFFRACTION	100
2.7254-2.7888	0.259452579869	143	0.25	1260	X-RAY DIFFRACTION	100
2.7888-2.8585	0.353366284049	136	0.261625676018	1287	X-RAY DIFFRACTION	99.9297752809
2.8585-2.9358	0.27013699493	141	0.253116935478	1283	X-RAY DIFFRACTION	100
2.9358-3.0222	0.269957948424	145	0.253153197028	1289	X-RAY DIFFRACTION	99.860724234
3.0222-3.1197	0.293218397793	141	0.248580284841	1279	X-RAY DIFFRACTION	99.9296270232
3.1197-3.2312	0.290543693412	145	0.231417326962	1338	X-RAY DIFFRACTION	99.8653198653
3.2312-3.3605	0.244568167416	140	0.206307925161	1223	X-RAY DIFFRACTION	100
3.3605-3.5134	0.225995518036	141	0.211635580339	1294	X-RAY DIFFRACTION	100
3.5134-3.6986	0.225998011468	144	0.188648258075	1282	X-RAY DIFFRACTION	99.9299229152
3.6986-3.9302	0.254510641446	147	0.196884922692	1314	X-RAY DIFFRACTION	100
3.9302-4.2335	0.217915465313	139	0.186534354125	1273	X-RAY DIFFRACTION	100
4.2335-4.6593	0.195371453069	141	0.155880641378	1273	X-RAY DIFFRACTION	99.4374120956
4.6593-5.3328	0.191566606713	140	0.183229960856	1274	X-RAY DIFFRACTION	100
5.3328-6.716	0.260622241812	143	0.202266702898	1294	X-RAY DIFFRACTION	99.8610145935
6.716-10	0.224071168972	143	0.203340523069	1265	X-RAY DIFFRACTION	98.3240223464

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	6.64627521271	-4.37288404183	2.20109181666	8.52020471042	-3.27029208707	7.30913481734	0.0406185233956	0.643654812003	-0.0323373800418	-0.974043540639	0.52609726792	1.59205787838	0.133843445245	-0.591939047241	-0.508475613884	0.423878130588	-0.110796868389	-0.116321083805	0.40677660612	0.187593918427	0.568277698225	41.8484058227	16.2331515182	152.012441072
2	6.60264555475	-0.359527422149	-0.459235900853	2.71417781697	-0.3067906617	2.32707371368	0.0792939393518	-0.231383827449	0.334929599281	-0.0846256323236	-0.0243282807651	0.210142033471	0.0927119877077	-0.0866665683826	-0.112826308624	0.238480744178	-0.0621348931236	-0.0464611596319	0.307415314164	-0.00924994940651	0.329305585128	52.4535582277	15.1888993278	159.363207967
3	3.12322959952	1.63135349407	2.67692642646	3.57648752889	2.34969308545	3.09876634521	0.200375425961	-0.280491727267	0.194449573371	0.321966828573	-0.237127423301	0.694988517614	-0.0692920823508	-0.196168510778	0.0580483049295	0.320296113402	-0.0425504218102	0.110963375479	0.380101698696	-0.0335800696847	0.362513198347	48.0381285817	18.7151224687	169.02567754
4	5.87339307207	0.222673602348	2.04121344719	6.85861411767	-2.08770605883	5.46100152117	0.0502275970788	-0.341975477986	0.249311988262	1.26505584759	-0.1409455121	0.353066506276	0.00245880192865	-0.542306293647	0.0883239182811	0.702428229422	-0.113027228506	0.0959199391264	0.50024433522	-0.0213501694818	0.297485402723	55.1449777192	20.6343923922	180.84259241
5	6.55463511336	-3.41308893862	-1.20893775279	8.43074616352	2.24681097441	4.91022324886	0.259295299159	0.469792341859	-0.32255893199	-1.44361775433	0.345990672277	-1.25332629003	-0.314958263079	0.168545393709	-0.471724446584	0.442396128866	-0.135841456581	0.150916920034	0.495446137843	-0.119512778868	0.510027986516	31.2812854577	9.87765665623	152.100696964
6	8.57046801554	-1.01671717474	0.474159013942	6.45621063089	0.70575863166	3.05259602565	0.00551814226662	-0.398136476408	0.408373164292	0.0830891060547	-0.116106343939	-0.22282306691	-0.20864350555	-0.0944746211745	0.105439814077	0.244829798824	0.0185523595899	0.0145743915266	0.359966795801	0.00799595317022	0.247092146843	19.193736032	16.5084290535	162.304420077
7	6.22527167649	-5.95889550024	2.82982650647	8.59470201866	-2.19868871536	2.2794225915	0.0415525897897	0.107853052163	-1.26236161578	-0.495864302255	0.29972633285	0.178881448867	-0.0636376732598	-0.0130722461114	-0.27628617833	0.289901163682	-0.084704790013	0.0130239323985	0.364678644512	-0.0265381385636	0.393249938119	21.685195939	4.95093003429	153.845786562
8	6.81636288327	-4.94240421127	-1.43260476999	5.19935219133	2.58710414208	4.34401831221	-0.775772066598	-0.0828967374652	-2.26182845691	-0.301554257243	0.0260892607736	-0.583384523803	1.06438766376	0.303008533191	0.660251455445	0.441417744788	-0.0119414136166	0.0368439903876	0.449520984561	-0.0359114050057	0.884116336234	32.657734334	-4.81392990358	161.022072678
9	1.79609811788	-1.59660629117	-0.443734047703	3.02351712422	0.209388998872	1.32669523118	0.00120942821169	-0.00980885160177	0.0928934893246	0.422041798465	-0.0302977614273	-0.788710559399	0.0128258250143	0.0947023738187	0.16187427832	0.227979600604	-0.0288450029492	-0.0841271692678	0.311471520576	0.0385345637105	0.338094797489	28.2676484312	6.64346492415	166.745275546
10	2.32794257818	2.54152024917	-2.09729643976	3.4491156104	-4.09044209124	7.12711651587	-0.00815575268354	1.12525587567	-0.154957704742	-0.202617353616	0.332584172453	-0.191976124101	-0.352477371504	0.374553601976	-0.380693337706	0.454205658679	-0.0528208405957	-0.0371087737176	0.485445895098	-0.0290462857082	0.29486072869	20.7745447824	7.69844664911	173.341272571
11	4.05884206592	3.61880075864	1.53136652562	8.38316857806	-2.24494845272	3.30847126135	0.152297260825	-0.874276564532	0.809868155416	0.677917746552	-0.401901599712	0.259952750087	-0.57160161779	0.170908906691	0.188049355535	0.656166037794	-0.14064580906	0.0193184948465	0.373033898509	-0.144215402819	0.413978024014	17.7730313439	13.6894869802	178.454428654
12	9.34305546357	-3.03539647198	-2.42369912181	2.42631906485	3.02233065275	5.53059747353	-0.0671134193185	-0.816483173351	-0.511958335387	1.23508476413	-0.287442538394	-0.0444667006312	0.197013267213	0.456279547414	0.389119070365	0.698782397409	-0.0812717726676	-0.116403304429	0.525212672268	0.0551984754118	0.330216814137	19.5772223932	1.93071501759	181.839678722

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 21 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 through 98 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 99 through 137 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 138 through 161 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 21 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 22 through 67 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 68 through 91 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 92 through 98 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 99 through 125 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 126 through 137 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 138 through 144 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 145 through 161 )

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