PDB-8v3e: Structure of Myroides odoratus phage Tad2 in apo state

ID or keywords:

Entry

Database: PDB / ID: 8v3e

Title

Structure of Myroides odoratus phage Tad2 in apo state

Components

Tad2

Keywords

VIRAL PROTEIN / His-ADPR / phage / anti-defense / sequestration

Biological species

Myroides odoratus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.39 Å

Authors

Lu, A. / Kranzusch, P.J.

Funding support

United States, 2items

Citation

Journal: Nature / Year: 2025
Title: TIR domains produce histidine-ADPR as an immune signal in bacteria.
Authors: Sabonis, D. / Avraham, C. / Chang, R.B. / Lu, A. / Herbst, E. / Silanskas, A. / Vilutis, D. / Leavitt, A. / Yirmiya, E. / Toyoda, H.C. / Ruksenaite, A. / Zaremba, M. / Osterman, I. / Amitai, ...

History

Deposition	Nov 27, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jun 4, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jun 25, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8v3e.cif.gz	171.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8v3e.ent.gz	113.9 KB	Display	PDB format
PDBx/mmJSON format	8v3e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v3/8v3e ftp://data.pdbj.org/pub/pdb/validation_reports/v3/8v3e	HTTPS FTP

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Related structure data

Related structure data	8r66C 9eibC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

E: Tad2

F: Tad2

A: Tad2

B: Tad2

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	93.206, 93.206, 235.549
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	155
Space group name H-M	H32
Space group name Hall	R32"
Symmetry operation	#1: x,y,z #2: -y,x-y,z #3: -x+y,-x,z #4: x-y,-y,-z #5: -x,-x+y,-z #6: y,x,-z #7: x+1/3,y+2/3,z+2/3 #8: -y+1/3,x-y+2/3,z+2/3 #9: -x+y+1/3,-x+2/3,z+2/3 #10: x-y+1/3,-y+2/3,-z+2/3 #11: -x+1/3,-x+y+2/3,-z+2/3 #12: y+1/3,x+2/3,-z+2/3 #13: x+2/3,y+1/3,z+1/3 #14: -y+2/3,x-y+1/3,z+1/3 #15: -x+y+2/3,-x+1/3,z+1/3 #16: x-y+2/3,-y+1/3,-z+1/3 #17: -x+2/3,-x+y+1/3,-z+1/3 #18: y+2/3,x+1/3,-z+1/3

Components on special symmetry positions

ID	Model	Components
1	1	B-133- HOH

#1: Protein	Tad2 Mass: 9906.152 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myroides odoratus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.48 Å³/Da / Density % sol: 50.5 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: magnesium chloride, sodium acetate, PEG 400

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Data collection

Diffraction	Mean temperature: 193 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 13, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.39→45.57 Å / Num. obs: 109160 / % possible obs: 99 % / Redundancy: 6.9 % / B_iso Wilson estimate: 22 Å² / R_pim(I) all: 0.039 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.39→2.48 Å / Num. unique obs: 15778 / R_pim(I) all: 0.071

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
Aimless		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.39→45.57 Å / SU ML: 0.2886 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 27.083
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2733	1580	10.01 %
R_work	0.227	14198	-
obs	0.2316	15778	99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 25.61 Å²

Refinement step

Cycle: LAST / Resolution: 2.39→45.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2530	0	0	206	2736

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	2589
X-RAY DIFFRACTION	f_angle_d	0.4319	3504
X-RAY DIFFRACTION	f_chiral_restr	0.0387	373
X-RAY DIFFRACTION	f_plane_restr	0.0026	440
X-RAY DIFFRACTION	f_dihedral_angle_d	12.3042	932

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 (%)
2.39-2.47	0.3052	138	0.2663	1236	X-RAY DIFFRACTION	96.42
2.47-2.56	0.2888	144	0.2493	1279	X-RAY DIFFRACTION	100
2.56-2.66	0.316	144	0.2475	1283	X-RAY DIFFRACTION	99.86
2.66-2.78	0.2935	139	0.2473	1276	X-RAY DIFFRACTION	99.72
2.78-2.93	0.3173	146	0.237	1265	X-RAY DIFFRACTION	99.58
2.93-3.11	0.248	145	0.2317	1306	X-RAY DIFFRACTION	99.59
3.11-3.35	0.3131	144	0.2384	1277	X-RAY DIFFRACTION	99.58
3.35-3.69	0.2716	147	0.2212	1310	X-RAY DIFFRACTION	99.73
3.69-4.22	0.2505	144	0.1966	1289	X-RAY DIFFRACTION	99.03
4.22-5.32	0.2029	145	0.1939	1317	X-RAY DIFFRACTION	99.12

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	0.196177402629	0.058846744069	-0.00516963344677	0.0765015894493	0.284308916062	1.734336443	0.204119433418	0.223213959323	0.189210286109	-0.0657277073086	-0.102867279775	-0.169513067459	-0.420385336813	0.394470235294	0.0939624442982	0.296343131868	0.092473061747	0.110848428323	0.180273058956	0.144928735082	0.22460068695	30.092281975	5.45632555827	10.9596404629
2	0.730168445957	0.260320844854	-0.032669273228	0.940162824951	0.661370940983	0.844194078753	0.151638197657	-0.179812873912	-0.101530988221	0.191460256917	-0.193512910824	0.0126310574451	0.23528248863	0.176231675383	-0.0677292909923	0.111796451873	0.0367567029431	0.00995247939303	0.144183945375	0.0112353512129	0.131870167875	20.0841256138	-5.56608530349	28.7355764826
3	0.439361264503	0.309003131439	0.528539664183	0.266218124059	0.33188606452	1.43209653207	-0.0279424504558	0.111777266266	-0.0180814160591	0.190758360441	0.107502624171	-0.0224954054052	0.055594719763	0.263729934018	-0.00874208932237	0.134801144034	0.0249714881923	0.0386446572818	0.0799809004504	0.00904918957425	0.132548709353	31.1521260835	-24.4792088475	28.1198926274
4	0.457080955646	-0.0129527216789	0.181374046719	0.0543038301462	0.000238777731145	0.0601335623932	0.192857794376	-0.0192374922396	-0.340690721327	0.267085022666	0.0113667323594	0.222198897877	0.146171147555	-0.319169294122	0.00606111119896	0.275723384337	-0.000300839385989	-0.00698335423339	0.418182138886	-0.0105921431259	0.184457621637	8.59038389039	-33.5687496634	9.25738962739
5	0.0108249570278	-0.018963065987	0.00769716869881	0.0412529246858	-0.00894050480898	0.00745011329938	0.0326669406093	0.0885861477516	-0.224262076837	-0.0108843747681	-0.0151488266724	-0.102400537022	0.0612535870981	-0.204789781292	-0.000200810562269	0.609040211887	-0.144054225182	0.069767754982	1.04617828776	0.0531413478566	0.52035831434	6.8715727597	-29.6209634696	3.66759011805
6	1.30359628922	-0.218886015346	0.0616843606099	0.598739053057	-0.86022720746	1.28627641987	0.288724046932	0.214016582929	-0.0513085947899	-0.188773038044	0.165354416934	0.107595172645	0.0319939911055	-0.15340396772	0.590992954061	0.129976442094	0.091771568006	-0.0456342813607	0.20973797634	-0.0536094712346	0.184109129345	17.0182608704	-29.9250018353	9.9866598561
7	0.942641462463	0.242617747389	0.131244430885	0.713176455889	-0.650643077941	0.754825302648	0.184725814914	-0.400724262382	0.274308904416	0.384246700267	-0.115850618541	0.205765168982	-0.248629010531	-0.0457211903562	0.189185154275	0.0893005561516	0.00799246037945	-0.044722558012	0.12046819836	0.00780127611136	0.148755078974	26.7888329493	-21.2577829171	28.4206632504
8	1.3918792312	0.819820643017	0.391638030412	0.598446147449	-0.00629730672359	0.643881049917	0.0925485628274	0.395642265512	-0.484613839271	-0.320155464964	0.0328397365869	-0.452071772699	0.156309743757	0.243426559062	0.141836818735	0.145044915537	0.00860780476579	0.00342146710202	0.198952712013	0.055133333055	0.0894745116594	40.401953358	-16.4836181061	13.6842107571
9	0.660182825413	0.462578063493	0.0212820762108	1.21352695459	-0.743481756754	0.693869881299	-0.167422311464	0.561842012415	-0.348024737354	-0.438749333102	-0.0231479851282	-0.0441531575181	0.363562026845	0.228753605971	-0.202923257301	0.159776350189	-0.0272693674208	-0.0966493731939	0.324902050552	-0.0105180282565	0.194475116262	34.5961756439	-10.8841654495	7.65687495082
10	0.0087553578977	-0.0386335706926	0.0354307374666	0.48061816314	-0.181269742653	0.375076208516	-0.310619737843	-0.283879521849	0.553538279787	-0.139627195726	0.15097524873	0.0692995769206	-0.177583060391	0.225318510142	-0.0973195957187	0.14749737858	-0.0367837930319	-0.0288542631489	0.330776066013	-0.121121175623	0.267001483948	36.466146203	1.35447036964	29.3341940587
11	0.000231030760296	-0.0343040801593	-0.0319013469606	0.130094939223	0.126779074114	0.118146652661	0.0833059725779	0.287664954964	0.16236780903	-0.230899861242	-0.197424985738	0.353411057306	-0.139306343111	-0.241263566269	-0.0684495990362	0.219587123132	0.0249522646767	-0.041322928222	0.289249015754	0.0626039982973	0.176707143576	30.1812748369	-9.19317069255	12.275535806
12	0.0387960486787	0.0541139138235	0.104942429514	0.177911650052	0.283077175931	0.424232710086	0.0234529968247	0.123902349236	-0.0298334629201	-0.292624110291	0.132396954365	-0.362617989872	0.0419130404772	0.20683760603	0.0383352498084	0.181930186215	0.0646236534281	0.0770902106243	0.337999350486	0.0318344764592	0.216406812973	38.6225064189	-18.1253370044	7.87990507769
13	1.90362310995	1.68226557755	-0.782549854912	1.60363235597	-0.611546213036	1.74813376761	0.265530307767	0.183401929588	0.402315313633	-0.138617145702	-0.176726785341	0.618963184193	-0.169906372597	-0.318203880299	0.317357766893	0.0863559846634	0.0724226363892	-0.0703042352912	0.1753956545	0.0201547713655	0.0927242102408	7.31689166696	-10.340793306	12.584397706
14	0.419647236431	0.0141691836086	-0.0442356329814	-0.0100052513644	-0.016238103898	0.052844167478	0.193110637821	-0.240904952568	0.0461391176489	-0.0349286197943	-0.123403062726	0.13541175962	0.0106626991308	-0.133367723324	0.434760635995	0.136145066802	0.0751415470054	0.133341036482	0.111854091435	-0.275096261749	-0.51579803669	10.6798499472	-18.2078304842	8.89451889978
15	0.252502680176	-0.0304920735378	-0.326966168943	0.455884522057	-0.399903145451	0.792076959201	0.339512603989	0.236199488477	0.0425224209077	-0.150042448525	-0.0752607063357	0.227455093261	0.227790031139	-0.0249115932587	0.179186635753	0.185117825531	-0.0282714500019	-0.0314714558169	0.170193209867	-0.0307984667704	0.252955062612	14.3704625549	-33.4610312952	31.1887897316
16	0.29462300728	-0.104391438238	0.313793473373	0.759582385765	0.116764511312	0.452381779449	0.12604426131	0.207305205822	0.116128924073	-0.632547601741	-0.00726205609939	-0.0960978553084	-0.087356069439	0.20459570841	0.154534012597	0.142574706019	0.0524620597428	-0.040876946799	0.217242854543	-0.00790467382756	0.0990877966801	14.0167445978	-14.9285039467	11.22205982
17	0.294170940673	0.252359533507	0.0307884360877	1.64602320723	-0.662066604711	1.15017790445	0.0232666987337	-0.25076607465	0.266107408945	0.456947272239	-0.204471779294	-0.183694036011	-0.470606850536	-0.337929290421	-0.858760260654	0.162661478318	0.0631044268138	-0.0373177255428	-0.0760141182144	0.014562664985	0.18150093333	15.5528231728	-2.07952576653	28.6005906707

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 'B' and (resid 35 through 58 )	B	D	35 - 58	33 - 44
2	2	chain 'B' and (resid 59 through 88 )	B	D	59 - 88	45 - 74
3	3	chain 'E' and (resid 3 through 34 )	E	A	3 - 34	1 - 32
4	4	chain 'E' and (resid 35 through 47 )	E	A	35 - 47	33 - 45
5	5	chain 'E' and (resid 48 through 52 )	E	A	48 - 52	46 - 50
6	6	chain 'E' and (resid 53 through 58 )	E	A	53 - 58	51 - 56
7	7	chain 'E' and (resid 59 through 88 )	E	A	59 - 88	57 - 86
8	8	chain 'F' and (resid 3 through 21 )	F	B	3 - 21	1 - 19
9	9	chain 'F' and (resid 22 through 34 )	F	B	22 - 34	20 - 32
10	10	chain 'F' and (resid 35 through 58 )	F	B	35 - 58	33 - 43
11	11	chain 'F' and (resid 59 through 80 )	F	B	59 - 80	44 - 65
12	12	chain 'F' and (resid 81 through 88 )	F	B	81 - 88	66 - 73
13	13	chain 'A' and (resid 3 through 24 )	A	C	3 - 24	1 - 22
14	14	chain 'A' and (resid 25 through 34 )	A	C	25 - 34	23 - 32
15	15	chain 'A' and (resid 35 through 58 )	A	C	35 - 58	33 - 56
16	16	chain 'A' and (resid 59 through 88 )	A	C	59 - 88	57 - 86
17	17	chain 'B' and (resid 3 through 34 )	B	D	3 - 34	1 - 32

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