PDB-6xb4: Structure of PrGV poxin in post-reactive state with Gp[2'-5']Ap[3']

ID or keywords:

Entry

Database: PDB / ID: 6xb4

Title

Structure of PrGV poxin in post-reactive state with Gp[2'-5']Ap[3']

Components

Poxin

Keywords

HYDROLASE / Poxin / Nuclease / Granulovirus / Baculovirus / Innate Immunity / cGAS / cGAMP / STING

Function / homology

Family of unknown function (DUF5887) / 2',5'-GpAp / Uncharacterized protein

Function and homology information

Biological species

Pieris rapae granulovirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.9 Å

Authors

Eaglesham, J.B. / McCarty, K.L. / Kranzusch, P.J.

Citation

Journal: Elife / Year: 2020
Title: Structures of diverse poxin cGAMP nucleases reveal a widespread role for cGAS-STING evasion in host-pathogen conflict.
Authors: Eaglesham, J.B. / McCarty, K.L. / Kranzusch, P.J.

History

Deposition	Jun 5, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 25, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6xb4.cif.gz	408.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6xb4.ent.gz	277.6 KB	Display	PDB format
PDBx/mmJSON format	6xb4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6xb4_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	6xb4_full_validation.pdf.gz	1.4 MB	Display
Data in XML	6xb4_validation.xml.gz	39.3 KB	Display
Data in CIF	6xb4_validation.cif.gz	55.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xb/6xb4 ftp://data.pdbj.org/pub/pdb/validation_reports/xb/6xb4	HTTPS FTP

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Related structure data

Related structure data	6xb3C 6xb5C 6xb6C C: citing same article (ref.)
Similar structure data	5kss-d 4ovi-d 1ii5-1 6gqi-2 4nbk-d 4up2-2 3hlx-d 3vdn-d 1otw-d 3tfz-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Poxin

B: Poxin

C: Poxin

D: Poxin

hetero molecules

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

1

A: Poxin

B: Poxin

hetero molecules

defined by author
Evidence: gel filtration
46.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Poxin

D: Poxin

hetero molecules

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

Unit cell

Length a, b, c (Å)	77.470, 58.140, 100.698
Angle α, β, γ (deg.)	90.000, 108.548, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Poxin Mass: 23032.080 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: N-terminal serine residue is an expression tag. / Source: (gene. exp.) Pieris rapae granulovirus / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: V9XTR0
#2: Chemical	ChemComp-9BG / 2',5'-GpAp / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate Mass: 692.427 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₀H₂₆N₁₀O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 749 / 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: 2.34 Å³/Da / Density % sol: 47.44 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 200 mM magnesium chloride, 100 mM Tris-Cl, 21-25% PEG-3350 PH range: 8.3 - 8.7

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.9→38.64 Å / Num. obs: 66856 / % possible obs: 99.4 % / Redundancy: 7 % / B_iso Wilson estimate: 27.42 Å² / CC_1/2: 0.997 / R_pim(I) all: 0.057 / Net I/σ(I): 9.7
Reflection shell	Resolution: 1.9→1.94 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4149 / CC_1/2: 0.472 / R_pim(I) all: 0.934

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
XDS		data reduction
Aimless		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.9→38.64 Å / SU ML: 0.1795 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.651
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2068	2006	3.01 %
R_work	0.1826	64535	-
obs	0.1833	66541	98.97 %

Solvent computation

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

Displacement parameters

B_iso mean: 35.32 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→38.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6216	0	138	749	7103

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0024	6506
X-RAY DIFFRACTION	f_angle_d	0.5676	8854
X-RAY DIFFRACTION	f_chiral_restr	0.0475	968
X-RAY DIFFRACTION	f_plane_restr	0.0027	1117
X-RAY DIFFRACTION	f_dihedral_angle_d	17.3325	2307

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 (%)
1.9-1.95	0.2837	133	0.2759	4331	X-RAY DIFFRACTION	93.41
1.95-2	0.2638	147	0.2481	4544	X-RAY DIFFRACTION	98.7
2-2.06	0.3024	133	0.2378	4586	X-RAY DIFFRACTION	99.33
2.06-2.13	0.2363	158	0.2191	4572	X-RAY DIFFRACTION	99.35
2.13-2.2	0.2533	122	0.2098	4679	X-RAY DIFFRACTION	99.79
2.2-2.29	0.25	149	0.2063	4588	X-RAY DIFFRACTION	99.43
2.29-2.39	0.2346	141	0.204	4574	X-RAY DIFFRACTION	98.93
2.39-2.52	0.2319	150	0.2061	4627	X-RAY DIFFRACTION	98.82
2.52-2.68	0.2552	144	0.197	4606	X-RAY DIFFRACTION	99.79
2.68-2.88	0.216	142	0.1945	4633	X-RAY DIFFRACTION	99.73
2.88-3.17	0.2092	139	0.1777	4663	X-RAY DIFFRACTION	99.81
3.17-3.63	0.1813	151	0.1686	4659	X-RAY DIFFRACTION	99.11
3.63-4.58	0.1721	146	0.1412	4688	X-RAY DIFFRACTION	99.94
4.58-38.64	0.1691	151	0.1679	4785	X-RAY DIFFRACTION	99.44

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	0.711420272967	0.734233932144	-0.662283375678	1.24669538512	-0.304763169354	1.30994899123	-0.120279289075	0.233957131771	0.0643618938438	-0.0873183436112	0.141970275856	0.0617334388909	-0.0151777099574	-0.0853639166573	0.000218384818383	0.18561467761	0.0134370222266	-0.00527884885156	0.195152231292	0.0312541724651	0.207655132811	-4.9566985747	10.9602007701	20.7216541936
2	0.788325269684	0.202963753524	-0.244818830555	0.429469188709	-0.454258246618	0.438669091681	0.128012648279	0.026329355615	0.159688596133	0.194885613056	-0.0134178718448	-0.0375725056821	-0.199585102213	0.0668178730542	0.00458303352326	0.279940774026	-0.0181804348546	0.00680310439475	0.168734855393	-0.0227556027829	0.224374943061	-5.894930897	10.327613366	35.9974061681
3	0.493367086351	-0.54251321491	0.458733249866	1.01356530459	0.0299706609565	1.29679676055	0.00632124776319	-0.152039452434	-0.00206842184353	0.210967693708	0.0198058463624	0.136408377295	-0.125234104703	-0.0430698867548	-9.2465891127E-5	0.334853777888	-0.0137926990075	0.0591055140412	0.187196077345	-0.00975018098874	0.185352473389	-15.0021126723	3.37073156638	50.9506733802
4	0.46077471343	-0.134173485524	-0.297481402822	0.200332354966	-0.144666937972	0.398368631251	0.341553142419	-0.128996540619	0.100197906102	0.0624321256898	-0.182900033982	0.0343147213566	-0.319623068365	0.120610452005	0.037213906713	0.29662792508	0.00258341008731	0.0295418406626	0.154530135736	-0.0138413445043	0.236383915351	-8.29533635393	4.21534631302	41.7282909524
5	0.538512878069	-0.149564085621	-0.381266153248	0.540913888331	0.15035942223	0.274814741208	-0.20091603065	-0.62790858512	-0.226594779035	0.574257296089	0.108434801449	-0.0425845965204	0.247574474813	0.222814699513	-0.00876210798731	0.318919628703	-0.00983524235379	-0.00941867642969	0.326093325991	0.0529556073877	0.278861085178	-4.0558208146	-15.23309538	58.424078995
6	0.365571587935	-0.494544320892	0.324519061329	0.520139516466	-0.310404199224	0.823593531938	0.0263157250236	0.0768130897196	0.0156442574488	-0.0277074452539	-0.131702323293	-0.0734100148448	0.0287566560828	0.312366863148	-0.0124313236623	0.201172583323	-0.016247429315	-0.0132462139295	0.248864993567	0.0450995019394	0.217490772049	6.24520014044	-11.9593747301	46.0582414762
7	0.926177951769	-0.312501043253	-0.318920573863	0.401634179694	0.0692343389634	0.454316333646	-0.0568043448914	0.214384074685	-0.266266339595	-0.0275336676717	0.0461372277069	-0.221592283454	0.109278689287	0.652204977038	-0.150112374945	0.226915163313	0.00942371465484	-0.0111339079564	0.402843549748	0.0398542126004	0.240148654308	14.0437241385	-17.9087137266	49.6468451996
8	0.566027500059	0.533750362687	0.149863643958	0.696548568586	0.148300235097	0.733032180552	0.205797638749	0.209950571878	-0.25642276702	0.0058273026907	0.0824470105448	-0.438596919849	0.470822933515	0.422911544307	0.0310901146937	0.340774068634	0.0779290737815	-0.039900394501	0.344183291566	-0.00203752000379	0.297951267575	9.5124618286	-21.6783366791	41.5352468752
9	0.196334430416	-0.0412604758383	-0.138712701285	0.0400133005854	-0.101090048976	0.3338043073	0.0988441109207	-0.17356301639	-0.0553929174735	-0.0480443263877	-0.100996091791	-0.0162134691765	0.00873014761116	0.115244001994	0.0026257525088	0.295417180787	0.00358756412109	-0.0183243992379	0.181903835949	0.00838006578518	0.227251566336	-3.14909490569	-7.16842126189	43.7168492133
10	0.348374527706	0.245432004229	-0.117534143521	0.156442360785	-0.0801773188868	0.0691673683388	0.00514929126431	0.726206258817	-0.336557776877	-0.454510688339	-0.251186564099	0.160049720205	-0.109667054665	-0.321665020247	-0.0567904818751	0.534893491087	0.0526597542698	-0.0992970059603	0.392054065872	-0.108549358703	0.354663043709	-12.1984942648	-14.2784027665	26.3951330471
11	0.142439951353	-0.304269095376	-0.0905649312576	1.27773824877	-0.0777347748815	0.241085941604	-0.159896681871	0.215792829537	0.27460834331	-0.794555309746	-0.201218589266	0.891244193137	-0.520128508494	-0.605183003573	0.135066916367	1.00862099616	0.217246119408	-0.508743110759	0.634394036285	-0.25466763078	0.439472273547	-22.3928919342	-9.38277420778	22.6558229175
12	0.0206473079411	-0.0570042206272	-0.0649661512644	0.310766074395	-0.122564244251	0.831729486329	0.0485973083875	0.309778130402	-0.438415254719	0.0952217091916	-0.0949853431723	0.341080384893	0.590279942658	-0.364874519473	0.067225488525	0.311894619349	0.0185407983017	-0.0708214762739	0.232752653728	-0.0550254711744	0.296660346035	-15.553202606	-12.0295480426	34.753206676
13	0.520822521326	-0.324851235882	0.511148232124	0.245426275939	-0.312748821515	0.488546607956	0.219796076178	0.542892443159	-0.0403083911215	-0.324923055028	-0.189245217621	0.0875762418008	0.208357274332	0.0970396981285	0.00918867871559	0.314712454041	0.028365233226	-0.041769951354	0.221106173041	-0.0530196842243	0.24919477179	-9.78177034	-10.7626396445	31.3197115357
14	0.118610900893	-0.053780782839	0.13211488159	0.0993962884448	0.0438146932529	0.163844410204	0.438368374593	0.549153748755	0.0561691313439	-0.452453696956	-0.353345862791	-0.0360833496831	-0.14799800756	0.124386527162	-0.000234896045087	0.330076441002	0.0723117393021	-0.0170817222075	0.259816003271	-0.00427354371422	0.267755379309	-6.35565223378	-7.46471128869	31.7317592931
15	0.307211556999	-0.226135525008	0.000742300021951	0.510395479847	0.160423396464	0.314439298584	-0.165202002526	-0.0510790750399	0.165200584435	0.143078929213	0.145895293153	-0.296148658578	-0.285492789153	0.655030616722	-0.000566367990346	0.239633739579	-0.0485654689608	0.00238264707871	0.4495233289	-0.0280075897414	0.283480997027	43.0389799996	10.5296603934	15.1681373948
16	0.933449907954	0.0308469655046	0.404183173092	0.68420759345	0.310573957683	0.807410981998	-0.125386998115	-0.119088030384	0.110314685184	0.094487498574	0.0297027704068	-0.0338954508578	0.0640714705608	0.00768275027721	-0.000518886932718	0.228191198824	-0.0284662145502	-0.0173626230207	0.284144875352	-0.0381192076349	0.240602051719	29.8958405965	13.6872131756	23.6505959383
17	0.901040483194	-0.209030201487	0.640046385335	2.13546853834	-1.25966462853	1.1691197959	-0.342869444881	-0.151333179889	0.516062598071	0.34437586533	0.168553649238	0.310122646916	-0.651831800948	-0.0584443957136	0.040036076314	0.374755327041	-0.0278975507452	-0.0377082092122	0.33266528506	-0.0693398459659	0.394500622483	26.9341078844	21.8382121299	21.7206866184
18	0.0360232410464	-0.100095135316	-0.0838659588051	1.11241777123	0.175748265439	0.809541800568	0.0320462896838	0.177308080765	0.0761949066692	-0.149364613894	-0.0239582521526	0.201385859298	-0.262729060217	-0.461940621305	0.00604802489857	0.221923530481	0.0237786480645	-0.0311732719493	0.522442381855	0.0174109770032	0.300628629707	22.3185951798	8.66479319137	-2.62153339351
19	0.505813262763	0.233454263956	0.108396693642	0.819000829151	-0.496640882623	0.403513802159	0.182909682531	0.309459161935	0.212439047876	-0.295229381994	-0.112728116623	0.0358002172157	-0.378476923057	-0.0886999137559	-0.000127796020665	0.288515669638	-0.0341507076631	0.00667536098026	0.380048355223	-0.0166129604444	0.294768483585	23.3907052852	10.1097259804	-0.946432707892
20	0.18428504167	0.0927708099963	0.220201027766	0.148036129429	0.0316296172432	0.185878249947	-0.0222817440106	0.0669811147103	-0.216503607698	-0.0981278555952	-0.452793166605	0.565753553359	0.200795548898	-0.701913936143	0.000432627261859	0.334053796014	-0.0666118296158	-0.0114516153557	0.396556252779	-0.0546310559316	0.279306406315	20.943695283	7.3528307848	4.50348122521
21	0.0935591181462	0.0287651792948	0.0734016239519	0.253189324233	0.0875944894773	0.217937810106	0.113956689756	0.340631537722	0.0574402978281	-0.393163306011	-0.271011131854	0.4195367991	-0.237317346412	-0.340540340702	-0.000344836809119	0.401050363779	-0.00480617442916	-0.0572801753389	0.344084136602	-0.092775894144	0.328601062174	9.37644446448	-7.82899853656	-7.76860573272
22	0.818031816779	0.123095903432	0.405866924836	1.28306781826	0.347012537165	0.804911256294	0.127845676602	-0.0121518294563	-0.332134797147	-0.0533698399225	-0.0569549524095	0.181166747182	0.148542479897	0.0358006599003	-0.00183222896014	0.245381252898	-0.026070022959	-0.0249987003152	0.218848099237	-0.0484886647474	0.300742274512	7.08309619491	-9.99008338279	8.3258634206
23	1.3915937999	-0.436408655689	0.258235895703	0.901060907002	0.926991412202	1.22706958488	0.181169973465	0.202404741521	-0.528090088562	0.188035397074	-0.0744139223561	-0.0175598517539	0.221180782574	0.0395306577888	0.02883208754	0.28518942577	0.00961129054555	-0.0670534049362	0.164733985611	-0.0640632575009	0.364177907157	13.0023270915	-11.1592425783	7.69512801377
24	0.635659398074	0.321566627337	0.217726576479	0.140206703666	0.118895762493	0.166049965977	-0.266858050123	-0.358114510787	-0.07909594353	0.276117500293	0.465533334523	-1.56237377602	0.446428373509	0.661301154669	-0.088867546409	-0.143021188141	0.53177230559	-0.250905698731	0.362883087334	-0.293882765517	0.993151294785	41.0545123419	-8.05899904077	7.16565144438
25	0.425801441923	-0.306475505746	0.183615651058	0.643198903811	0.265203691985	0.328379536256	0.272330945453	0.0436807234397	-0.190837283837	0.042680244901	0.175918586425	-0.162466483803	0.21163769721	0.392154935999	0.0647858861562	0.297207850901	0.0330058573897	-0.0109483833665	0.327645332923	-0.0739196288169	0.308665113028	31.598141002	-7.53020760102	5.38296353049
26	0.540087226936	-0.181143651651	0.0936172543115	0.146934250947	0.0293870256746	0.037013620177	-0.0422106039023	-0.246101028645	-0.707801929231	0.0926721681315	-0.225330772064	-0.318421576619	0.162754413026	0.3544856442	0.000922251671632	0.267489663726	0.00227347600034	0.00932819807939	0.294882160933	-0.0288082319261	0.360999800144	27.4608434535	-5.54058313646	9.50494169263

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 88 )	A	A	1 - 88	1 - 88
2	2	chain 'A' and (resid 89 through 142 )	A	A	89 - 142	89 - 142
3	3	chain 'A' and (resid 143 through 175 )	A	A	143 - 175	143 - 175
4	4	chain 'A' and (resid 176 through 199 )	A	A	176 - 199	176 - 199
5	5	chain 'B' and (resid 0 through 16 )	B	B	0 - 16	1 - 17
6	6	chain 'B' and (resid 17 through 72 )	B	B	17 - 72	18 - 73
7	7	chain 'B' and (resid 73 through 88 )	B	B	73 - 88	74 - 89
8	8	chain 'B' and (resid 89 through 108 )	B	B	89 - 108	90 - 109
9	9	chain 'B' and (resid 109 through 124 )	B	B	109 - 124	110 - 125
10	10	chain 'B' and (resid 125 through 135 )	B	B	125 - 135	126 - 136
11	11	chain 'B' and (resid 136 through 152 )	B	B	136 - 152	137 - 153
12	12	chain 'B' and (resid 153 through 169 )	B	B	153 - 169	154 - 163
13	13	chain 'B' and (resid 170 through 183 )	B	B	170 - 183	164 - 177
14	14	chain 'B' and (resid 184 through 197 )	B	B	184 - 197	178 - 191
15	15	chain 'C' and (resid 2 through 26 )	C	C	2 - 26	1 - 25
16	16	chain 'C' and (resid 27 through 88 )	C	C	27 - 88	26 - 87
17	17	chain 'C' and (resid 89 through 108 )	C	C	89 - 108	88 - 107
18	18	chain 'C' and (resid 109 through 153 )	C	C	109 - 153	108 - 152
19	19	chain 'C' and (resid 154 through 183 )	C	C	154 - 183	153 - 175
20	20	chain 'C' and (resid 184 through 197 )	C	C	184 - 197	176 - 189
21	21	chain 'D' and (resid 2 through 21 )	D	D	2 - 21	1 - 20
22	22	chain 'D' and (resid 22 through 88 )	D	D	22 - 88	21 - 87
23	23	chain 'D' and (resid 89 through 123 )	D	D	89 - 123	88 - 122
24	24	chain 'D' and (resid 124 through 149 )	D	D	124 - 149	123 - 148
25	25	chain 'D' and (resid 150 through 183 )	D	D	150 - 183	149 - 171
26	26	chain 'D' and (resid 184 through 198 )	D	D	184 - 198	172 - 186

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