PDB-8tto: Structure of Hachiman anti-defense 1 (Had1)

ID or keywords:

Entry

Database: PDB / ID: 8tto

Title

Structure of Hachiman anti-defense 1 (Had1)

Components

Hachiman

Keywords

VIRAL PROTEIN / immune evasion / anti-defense / phage

Biological species

unidentified (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Ragucci, A.E. / Antine, S.P. / Kranzusch, P.J.

Funding support

United States, 1items

Citation

Journal: Nature / Year: 2024
Title: Phages overcome bacterial immunity via diverse anti-defence proteins.
Authors: Yirmiya, E. / Leavitt, A. / Lu, A. / Ragucci, A.E. / Avraham, C. / Osterman, I. / Garb, J. / Antine, S.P. / Mooney, S.E. / Hobbs, S.J. / Kranzusch, P.J. / Amitai, G. / Sorek, R.

History

Deposition	Aug 14, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 22, 2023	Provider: repository / Type: Initial release
Revision 1.1	Dec 6, 2023	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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 17, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3	Jun 5, 2024	Group: Structure summary / Category: audit_author / Item: _audit_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8tto.cif.gz	101.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8tto.ent.gz	65.5 KB	Display	PDB format
PDBx/mmJSON format	8tto.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8tto_validation.pdf.gz	428.7 KB	Display	wwPDB validaton report
Full document	8tto_full_validation.pdf.gz	428.8 KB	Display
Data in XML	8tto_validation.xml.gz	9.9 KB	Display
Data in CIF	8tto_validation.cif.gz	13.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tt/8tto ftp://data.pdbj.org/pub/pdb/validation_reports/tt/8tto	HTTPS FTP

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Related structure data

Related structure data	8smdC 8smeC 8smfC 8smgC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hachiman

B: Hachiman

C: Hachiman

D: Hachiman

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

1

A: Hachiman

B: Hachiman

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

2

C: Hachiman

D: Hachiman

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

Unit cell

Length a, b, c (Å)	30.938, 40.181, 45.291
Angle α, β, γ (deg.)	75.220, 89.420, 74.910
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#1: Protein	Hachiman Mass: 6219.039 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: prophage sequence isolated after integration into Bacillus toyonensis AFS058541 genome Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.11 Å³/Da / Density % sol: 41.68 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES pH 6.2, 30% PEG 4000

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00011 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00011 Å / Relative weight: 1
Reflection	Resolution: 2→37.45 Å / Num. obs: 13372 / % possible obs: 97.3 % / Redundancy: 1.8 % / B_iso Wilson estimate: 29.25 Å² / CC_1/2: 0.993 / Net I/σ(I): 4.9
Reflection shell	Resolution: 2→2.05 Å / Num. unique obs: 979 / CC_1/2: 0.49

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→37.45 Å / SU ML: 0.2962 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.0547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2554	1333	9.99 %
R_work	0.2153	12017	-
obs	0.2194	13350	97.2 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.07 Å²

Refinement step

Cycle: LAST / Resolution: 2→37.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1361	0	0	172	1533

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0014	1385
X-RAY DIFFRACTION	f_angle_d	0.4003	1865
X-RAY DIFFRACTION	f_chiral_restr	0.0407	217
X-RAY DIFFRACTION	f_plane_restr	0.0022	211
X-RAY DIFFRACTION	f_dihedral_angle_d	9.9705	511

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 (%)
2-2.07	0.3358	133	0.3237	1195	X-RAY DIFFRACTION	95.47
2.07-2.15	0.3179	130	0.2892	1172	X-RAY DIFFRACTION	96.37
2.15-2.25	0.3406	132	0.2674	1191	X-RAY DIFFRACTION	96.29
2.25-2.37	0.3131	133	0.2552	1202	X-RAY DIFFRACTION	96.88
2.37-2.52	0.2842	135	0.2474	1211	X-RAY DIFFRACTION	97.61
2.52-2.71	0.2799	133	0.2445	1199	X-RAY DIFFRACTION	97.58
2.71-2.99	0.2834	133	0.2308	1200	X-RAY DIFFRACTION	98.01
2.99-3.42	0.2637	136	0.2137	1225	X-RAY DIFFRACTION	97.7
3.42-4.31	0.2116	134	0.1703	1206	X-RAY DIFFRACTION	98.24
4.31-37.45	0.1952	134	0.175	1216	X-RAY DIFFRACTION	98.18

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	2.81883895967	0.322240909361	0.828540144127	2.21932919878	0.121582707787	0.551782044711	-0.0244853913329	-0.199422837623	0.161107127399	0.132039742509	0.0396084679391	-0.0876061541279	0.0392019540717	-0.232980491447	0.000166225167836	0.249103750948	0.0154580901644	0.00281663353617	0.283363146594	-0.0509717412373	0.246744002984	8.66888707012	43.5131464794	0.437422000126
2	1.12436106355	0.919430484936	0.53066113383	0.880382772072	0.079333594394	1.24544869517	0.380674748729	0.475334622708	-0.0564232415685	-0.516910270363	-0.096436242353	0.0794355600132	-0.0924337313096	-0.0518960660417	-8.88079983159E-5	0.359718201634	0.00269166246791	-0.00835450905619	0.3528933094	-0.0168972727342	0.337140447725	10.5567407385	57.4477973076	7.28898123306
3	1.20917542035	1.51111156407	-0.294464817381	1.89976578243	-0.122495266381	0.567459069955	0.14936806483	-0.159321622325	-0.0719346959989	0.186027648804	-0.346175060532	-0.873203867269	0.10954975228	-0.174100657733	-0.0214970009637	0.375512519655	0.00266422887382	-0.00411346983018	0.216574230027	0.00294612496418	0.266117535214	11.985400006	38.8925667938	-4.11308315578
4	0.866007082352	-0.22718218454	-0.50613382606	0.272920664035	0.205813194086	0.318215212936	0.206077487222	-0.353722172666	0.322435504179	-0.486807825229	-0.0600377932521	0.309583310854	-0.311243955906	0.270509213661	-0.0014798935296	0.289253288101	-0.0164892694266	0.0624615612387	0.247686611699	0.0349432739871	0.313282910228	15.7321251759	36.4041303652	-0.281921232719
5	0.528115332069	0.131272323766	0.433596837225	0.68153221281	-0.350423888267	0.536152103989	0.0862998128892	-0.078651833272	-0.134050514542	0.50806764996	0.0138342922262	0.130442092789	-0.164971187329	-0.22063294433	-9.8437253207E-5	0.283218100143	-0.0596791489542	-0.0138618683836	0.382465434717	0.0276956832858	0.266823810629	10.6022255407	32.9657393366	5.71803977527
6	0.16369785485	-0.230128091872	0.215008238649	1.3488925998	-0.507599137075	0.316100313224	-0.0532662112357	-0.261602032987	-1.33925970934	0.611965607489	0.0602651021985	-0.133139380038	0.0560962716131	-0.574054622698	0.0551532470485	0.293609461748	-0.0123374692037	-0.0466798719638	0.342546408136	-0.00726862307893	0.332839949753	10.7610685028	19.5852184788	13.1633110274
7	1.11496409968	0.266157215657	-0.039082679105	0.179846507967	0.204982119168	0.390937368602	0.0746126954918	0.649372273762	-0.0710025965573	0.326465438148	0.0964838916878	-0.218175718577	-0.140503147034	0.370667909867	-0.00174035952872	0.302200083706	-0.0353602145206	0.0195275546156	0.287808438172	0.0441595341463	0.252624941074	3.40979368864	24.4099521109	6.63450249889
8	2.71058060528	0.475056598144	-0.0214606651854	0.363692177666	0.465287046102	2.52983447855	0.350262925282	-0.0237653692923	0.240938692053	-0.306831908028	-0.384196468541	0.0299325683033	-0.0433043142402	0.344219825052	-0.005182363489	0.292057646606	-0.0521267334754	0.0194451438296	0.238763507442	-0.0165681307531	0.310515940316	13.9335040417	38.8648212737	-3.61165940052
9	2.90567081048	0.674536995178	1.42804720572	1.63555468908	-0.675553553762	1.3951218209	-0.0512474886842	-0.317844057015	0.105384533586	0.244609415239	0.137248172131	-0.0500300253158	0.0325617963391	-0.0469829336135	7.35219131466E-5	0.311820133182	0.0786898636746	-0.0027102604536	0.304059657365	-0.00403982243609	0.303473450618	18.8528419783	30.3586695575	22.6338201411
10	0.481725263427	-0.00675800783813	-0.524125893231	3.92481836863	0.722365752199	0.721117048869	-0.212027350878	0.476535160284	0.166571986287	-1.56037419173	-0.251839102006	1.54947329519	-0.66623960928	-0.408125887245	-0.0158060432254	0.337211440177	0.0089610924672	-0.0225165967094	0.324936470537	-0.0838899489906	0.350459935732	14.1512496111	47.7562741873	27.9873234549
11	-0.0101151100307	0.00558017973327	0.0052943404439	1.34654471963	0.272685764664	0.361258275516	0.369729606447	0.292193525268	0.120212991538	0.450949626071	-0.600960556799	-0.393508188854	0.374192607462	0.207688927459	-0.00360556875707	0.25128779274	0.0201944017996	0.0289773733034	0.33886060419	0.00459054241281	0.307595038684	23.9257087093	42.2985934678	30.2650482046
12	0.879322826775	-0.336367279328	-1.11661765516	0.273513951839	0.763251693689	2.16680656884	0.414683410515	0.258353278923	-0.156854945294	-0.205029158279	-0.579711460046	-0.141682592305	-0.402553790621	-0.591829738496	-0.185315066308	0.326939399621	0.0592273635554	-0.0254957869378	0.205373566591	0.0293152513096	0.309870317633	22.2769810334	27.4454799852	18.2083319808
13	1.06730878162	0.275854195943	0.290364660568	0.344873063484	-0.0919307309956	0.175023214584	-0.200296538278	-0.723395044923	0.404861287626	-0.0341180706462	-0.0643367689073	-0.0793814502429	-0.0241394876453	0.141135120794	-0.0178867282796	0.345824798833	0.0239693149906	0.0401024545359	0.269771938286	0.0182331644467	0.310906912059	26.4706680104	24.6659278676	22.4013185152
14	0.43908790226	0.187202011636	0.3907730908	1.90748273684	-0.0573712966151	0.361557121987	-0.0512884864101	-0.391670620088	0.049880484776	0.793103356888	0.170534605419	0.33967782786	-0.0447169243604	-0.262353279181	0.000367358923993	0.386434073145	-0.028855991124	0.00460627245562	0.325283773568	0.0470099055572	0.271598204096	19.8758458073	19.7752700201	28.0031662906
15	0.127901349107	-0.0531792195941	0.148800676107	0.890251126441	0.948177022376	1.34817613663	-0.531480762228	-0.115377165017	-0.547999053048	-0.201815705488	0.119261547862	0.140328579436	-0.321591654055	-0.254583797116	-0.0355010820087	0.244113398604	-0.0506209402904	-0.0264166165894	0.353192048884	0.0615155992264	0.347327919159	20.2101550027	7.11111873591	35.7641320155
16	0.593710323147	1.49038876055	0.116698435431	8.77566484435	-4.84415639899	5.32261627051	0.271825909626	0.192750523374	-0.334388283246	-1.23886767235	-0.309398350599	-0.280103332464	0.739688560761	0.679049980244	0.0892131373293	0.154370925387	-0.0330334861898	0.00151391264324	0.316667137199	0.0611385658324	0.280591770346	13.0023456904	11.5277456636	28.5799317247
17	0.705069666949	-0.0410708240007	-1.07327673802	1.12292522717	-0.182864723629	2.11483374412	0.332910924492	-0.104017456003	-0.0307258958755	0.764240996494	-0.578140699927	-0.238936086679	-0.287945445276	0.367501180436	-0.0401444979319	0.255327168649	0.00106303147562	-0.00344867501647	0.210558213752	0.0102073917357	0.232018216426	24.5941540834	23.9399869837	19.6836277492

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 3 through 23 )	A	A	3 - 23	1 - 21
2	2	chain 'A' and (resid 24 through 34 )	A	A	24 - 34	22 - 32
3	3	chain 'A' and (resid 35 through 44 )	A	A	35 - 44	33 - 42
4	4	chain 'B' and (resid 4 through 11 )	B	B	4 - 11	1 - 8
5	5	chain 'B' and (resid 12 through 23 )	B	B	12 - 23	9 - 20
6	6	chain 'B' and (resid 24 through 28 )	B	B	24 - 28	21 - 25
7	7	chain 'B' and (resid 29 through 34 )	B	B	29 - 34	26 - 31
8	8	chain 'B' and (resid 35 through 44 )	B	B	35 - 44	32 - 41
9	9	chain 'C' and (resid 3 through 23 )	C	C	3 - 23	1 - 21
10	10	chain 'C' and (resid 24 through 28 )	C	C	24 - 28	22 - 26
11	11	chain 'C' and (resid 29 through 34 )	C	C	29 - 34	27 - 32
12	12	chain 'C' and (resid 35 through 43 )	C	C	35 - 43	33 - 41
13	13	chain 'D' and (resid 3 through 11 )	D	D	3 - 11	1 - 9
14	14	chain 'D' and (resid 12 through 23 )	D	D	12 - 23	10 - 21
15	15	chain 'D' and (resid 24 through 28 )	D	D	24 - 28	22 - 26
16	16	chain 'D' and (resid 29 through 34 )	D	D	29 - 34	27 - 32
17	17	chain 'D' and (resid 35 through 43 )	D	D	35 - 43	33 - 41

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