PDB-9dbh: Structure of Hailong HalB in complex with oligodeoxyadenylate

ID or keywords:

Entry

Database: PDB / ID: 9dbh

Title

Structure of Hailong HalB in complex with oligodeoxyadenylate

Components

(DNA (5'-D(P*AP*AP*AP*AP*AP*A)- ...) x 4
HalB

Keywords

ANTIVIRAL PROTEIN/DNA / Hailong / nucleotidyltransferase / oligodeoxyadenylate / anti-phage defense / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-DNA complex

Function / homology

: / DNA

Function and homology information

Biological species

Rhodobacteraceae bacterium QY30 (bacteria)
DNA molecule (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.88 Å

Authors

Tan, J.M.J. / Melamed, S. / Cofsky, J.C. / Hobbs, S.J. / Kruse, A.C. / Sorek, R. / Kranzusch, P.J.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Structure of HalB in complex with oligodeoxyadenylate
Authors: Tan, J.M.J. / Melamed, S. / Cofsky, J.C. / Hobbs, S.J. / Kruse, A.C. / Sorek, R. / Kranzusch, P.J.

History

Deposition	Aug 23, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 7, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9dbh.cif.gz	463.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9dbh.ent.gz	315.7 KB	Display	PDB format
PDBx/mmJSON format	9dbh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9dbh_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	9dbh_full_validation.pdf.gz	2.1 MB	Display
Data in XML	9dbh_validation.xml.gz	44.3 KB	Display
Data in CIF	9dbh_validation.cif.gz	58.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/db/9dbh ftp://data.pdbj.org/pub/pdb/validation_reports/db/9dbh	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: HalB

B: HalB

C: HalB

D: HalB

E: DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3')

F: DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3')

G: DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3')

H: DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3')

hetero molecules

112 kDa, 8 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)	56.365, 133.269, 79.165
Angle α, β, γ (deg.)	90.000, 107.920, 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

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Protein , 1 types, 4 molecules ABCD

#1: Protein	HalB Mass: 26517.859 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacteraceae bacterium QY30 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria)

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DNA (5'-D(PAPAPAPAPAPA)- ... , 4 types, 4 molecules EFGH

#2: DNA chain	DNA (5'-D(PAPAPAPAPAPA)-3') Mass: 1834.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#3: DNA chain	DNA (5'-D(PAPAPAPAPAPA)-3') Mass: 1521.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#4: DNA chain	DNA (5'-D(PAPAPAPAPAPA)-3') Mass: 1207.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#5: DNA chain	DNA (5'-D(PAPAPAPAPAPA)-3') Mass: 894.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)

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Non-polymers , 2 types, 518 molecules

#6: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
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: 2.54 Å³/Da / Density % sol: 51.51 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.05 M KCl, 0.1 M HEPES pH 7.0, 12.5% PEG-4000

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 4, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9201 Å / Relative weight: 1
Reflection	Resolution: 1.88→75.33 Å / Num. obs: 87087 / % possible obs: 97.4 % / Redundancy: 7.2 % / R_pim(I) all: 0.047 / Net I/σ(I): 8.7
Reflection shell	Resolution: 1.88→1.99 Å / Num. unique obs: 12470 / R_pim(I) all: 0.86

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.88→37.66 Å / SU ML: 0.3212 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8655
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2218	2011	2.32 %
R_work	0.196	84589	-
obs	0.1966	86600	96.76 %

Solvent computation

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

Displacement parameters

B_iso mean: 49.32 Å²

Refinement step

Cycle: LAST / Resolution: 1.88→37.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6823	378	4	514	7719

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0036	7365
X-RAY DIFFRACTION	f_angle_d	0.6359	9979
X-RAY DIFFRACTION	f_chiral_restr	0.0414	1112
X-RAY DIFFRACTION	f_plane_restr	0.0062	1220
X-RAY DIFFRACTION	f_dihedral_angle_d	14.4306	2772

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 (%)
1.88-1.93	0.4617	127	0.4364	5508	X-RAY DIFFRACTION	88.67
1.93-1.98	0.3544	145	0.3546	5986	X-RAY DIFFRACTION	96.26
1.98-2.04	0.3209	141	0.2839	6028	X-RAY DIFFRACTION	96.88
2.04-2.11	0.274	137	0.2479	6055	X-RAY DIFFRACTION	97.21
2.11-2.18	0.2742	145	0.233	6067	X-RAY DIFFRACTION	97.09
2.18-2.27	0.2829	145	0.2591	6065	X-RAY DIFFRACTION	97.23
2.27-2.37	0.2399	139	0.2106	6055	X-RAY DIFFRACTION	97.34
2.37-2.5	0.2296	150	0.2005	6069	X-RAY DIFFRACTION	97.46
2.5-2.66	0.2276	139	0.1934	6083	X-RAY DIFFRACTION	97.51
2.66-2.86	0.2208	148	0.1981	6077	X-RAY DIFFRACTION	97.51
2.86-3.15	0.2539	146	0.2007	6160	X-RAY DIFFRACTION	97.77
3.15-3.6	0.226	149	0.1788	6077	X-RAY DIFFRACTION	97.56
3.6-4.54	0.1742	149	0.1575	6106	X-RAY DIFFRACTION	97.51
4.54-37.66	0.184	151	0.1728	6253	X-RAY DIFFRACTION	98.61

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	7.28886738729	3.40398316638	4.64185690658	4.72513488019	3.74883009988	5.08224058031	-0.391412316883	0.137431882631	0.17115836994	-0.138150289807	0.274912223438	-0.0769468062328	-0.0645072412249	0.437304098654	0.196490299874	0.317919880254	0.0165550615633	0.0383601256317	0.284038845727	0.0179631528371	0.263698108603	19.9831064852	-17.0329148822	29.8752432419
2	2.55611461013	1.62388416732	0.133709406522	5.31052928806	0.206568015156	5.03713217155	-0.0751252353306	0.921830914624	-0.984243333979	0.0820548914339	0.377715828603	0.471688270846	1.12211893089	-0.464672676052	-0.280088082918	0.58178568114	-0.029981987564	0.0800844603094	0.424170123325	-0.0272120040136	0.583465753292	16.0199262222	-24.5844202671	30.0170667406
3	5.7066753298	3.2263160733	-1.99461867915	3.04285429022	-0.147732658819	4.771509393	-0.47985823659	-1.19197049822	-0.723533977912	1.49410477909	0.34258141886	0.152157799707	0.545055000747	0.345129792556	-0.227840308488	0.964309477801	0.192809485546	0.0158957072911	0.538374480151	0.133187081609	0.657409809433	27.5445497423	-24.8865207833	36.2324260356
4	1.70633249306	-1.30500739502	-1.88012190902	5.10732963326	-1.23419772845	6.24213470175	-0.569637761315	-0.0332298220272	-0.343556001146	-0.0682329413425	0.235510162493	-0.498889148797	1.00835400441	0.14296301112	0.0206074604032	0.310801680945	0.0506229436357	-0.0292822002869	0.328900598597	-0.00514742076405	0.329214555592	30.7293232782	-18.2131033392	28.2574378795
5	1.8891326256	-0.173907621204	-0.386140805748	3.87444010099	2.06200093262	4.75984057724	-0.154258449809	-0.00578886469537	0.188304870082	-0.0667701511427	-0.0789608518714	0.136116111384	0.275006871283	-0.161768105567	0.238296007591	0.274476695701	0.03851168507	0.00177170372491	0.245545311628	-0.0130413996821	0.293680951871	23.3235411437	-15.1064705151	23.8913352986
6	2.33557851441	-0.60622681775	-0.867700114266	5.2739646037	3.00921988101	6.12850903181	0.0800420237312	0.0640827132187	0.23584221955	-0.584413668003	0.0312224294406	-0.378909437716	-0.481623693917	0.130149440264	-0.0159509314675	0.269263552446	0.00582964435092	-0.0130159413004	0.26398858852	0.0207201896336	0.289331537582	29.4424741138	-13.2640400167	17.0546033623
7	2.29899134748	-1.27550425724	0.892482641297	2.95923653916	-0.0874254860485	2.43016369069	0.278743923529	-0.0891013713453	-0.213092348021	0.77573462461	-0.335018991487	0.0372428262616	0.460921045107	0.269368320588	0.0161159378786	0.698488687809	0.0320432725052	0.0440849536394	0.309038509883	-0.0440717926566	0.310081806332	31.5954435542	-40.2668025196	18.1256537493
8	2.20828017013	-1.08764022319	1.37499669554	6.30253480439	-1.53795395139	2.5767312644	-0.0559577101243	-0.0743084656638	-0.0789629108722	0.195448133283	-0.00446823580175	0.236362102501	0.650593441593	-0.28461185469	0.090717294075	0.414064422071	0.00584386340135	0.0954911914178	0.193290460634	-0.052500107472	0.270877065779	24.6093591821	-32.9965659233	17.5379857411
9	3.55671647609	-0.0216944759085	0.483140257987	7.35826037603	-0.105847356041	3.42238372176	0.258264863815	0.467425465022	-0.101317895894	-0.392354288598	-0.370682335935	0.987486338049	0.399855618441	-0.354198631732	0.137287246535	0.489650499178	-0.00421003169493	-0.0340814508797	0.396421134471	-0.0769352485091	0.388658263147	16.1995959582	-29.7875123748	11.2353452624
10	4.04642798459	-1.90307756754	2.04423401519	4.4665323045	-1.08860909637	4.91891396937	-0.108000635453	-1.0236300894	-0.530679152512	1.66836819063	0.640062411112	1.93909083289	0.387698036269	-0.92930767179	0.0450699070946	0.882946395841	-0.0852397168276	0.285921914493	0.554608102901	-0.041905542843	0.673681228758	17.1640564656	-40.2262091767	23.0590661672
11	3.62422144071	-0.755168093832	0.659797158489	6.49967648514	-1.38247510377	4.5434580155	0.170225221631	0.0849852846158	-0.654869008116	0.0935622989977	0.0458368623129	0.590731088753	1.05697002532	-0.921341181749	-0.0594195554573	0.742550268053	-0.095241726957	0.0650209426964	0.41248313858	-0.0540011464602	0.515727282931	21.4651357465	-45.9464645897	14.0809895734
12	5.66275489842	-0.345689899344	1.28355388113	5.87242095685	1.4245464208	4.70018169189	0.399571020018	0.355882438421	-0.32596012426	0.360232169488	0.188443591946	-0.754023121729	0.357980380375	0.93593461746	-0.603098264861	0.546834656012	0.0739588282152	-0.0152003785521	0.351873750394	-0.0446713397393	0.344557066449	39.1233375965	-40.6419238338	15.3495612983
13	8.00122287828	-1.11408542727	0.458577646326	8.27749212887	-3.52194654184	6.15200384371	-0.697938767146	-1.22099383885	-0.326575835054	1.94531301948	0.256272066509	-0.840087558624	-0.949228667838	0.475670140842	0.348843517317	0.832008273878	0.112615514142	-0.0360122994299	0.431660743012	0.0190375342836	0.409083981034	35.7290313824	-36.6297616489	27.0928504689
14	4.25328524672	-0.0236598762001	-0.46284716154	3.61245313036	1.09850727687	7.2761965245	0.123500574844	0.093424604617	0.325767138056	-0.197272073687	-0.327724425034	0.37053831716	-0.445306667231	-0.931338530633	0.256002664895	0.288727051363	0.0542678916994	-0.0166386291024	0.346051773838	-0.0261971479357	0.30236581628	10.3152314447	-5.54594405606	14.3339418829
15	2.7070920688	0.0364653201968	0.245790284749	2.86244206899	-1.22411486009	4.42222610766	-0.029256561933	-0.0387637463344	0.258052333747	0.0486355467699	-0.000126078046064	0.0747704532769	-0.608995392619	-0.0635707978829	0.0113911855874	0.363273649229	-0.0128695173238	0.0261989105708	0.261128057319	-0.0317051375928	0.229282373411	22.6348120861	7.35471020171	0.787641153182
16	3.65068401874	-0.918886454498	-2.13627687078	3.00566856357	0.562152194554	6.04823789112	0.250668458478	0.477368366823	0.308660870205	-0.435298624698	-0.231841761369	0.0145294524924	-0.588879148075	-0.115949951473	0.00446370903138	0.268477317174	0.0189510083479	-0.0347992372207	0.317475813899	0.0267031273507	0.251093506391	3.16497097226	3.59922895514	35.24584466
17	4.49548910209	0.0252074122685	1.98825884859	4.04175288872	1.52163213829	4.52867584777	-0.242306905715	0.0249522338725	0.468425329279	-0.5420940135	-0.208895079801	0.475263434555	-0.838002544516	-0.44635808408	0.23101318931	0.370027909525	0.0875253819532	-0.0954055994777	0.377541921126	-0.100580479798	0.373009475319	-18.2734174588	7.02724425221	39.0007156783
18	4.00083021641	0.524447006822	-2.25759276614	4.19448078266	0.463560160481	5.12379999741	-0.311149232592	-0.0431388996801	-0.466064265728	-0.0454660962179	0.16400509013	-0.269531382481	0.663938636511	0.377823336367	0.162091711824	0.288883268197	0.0423661472109	0.0160605569911	0.27340863614	-0.00348348138055	0.284996145913	11.0046814704	-16.886003381	43.6668089378
19	3.77955279382	0.162489992661	-0.178460320929	2.86648546628	0.619451266034	5.16159164611	-0.382082772515	-0.433394877852	-0.166820144366	0.258502627946	0.161416602143	-0.213488291382	0.280505833391	0.750814871062	0.147410084981	0.279891393883	0.10165179059	0.0597794697802	0.416932352584	0.054200774102	0.267585894135	13.3806535081	-9.01261383487	59.4043944458
20	2.44828651424	0.658249971917	0.166069516848	6.6959058877	0.88996061772	3.48419064036	-0.54460315437	-0.288556049071	-0.342090474002	0.20612835554	0.21121345488	-0.62632734108	0.976788778274	1.3262328679	0.259360003318	0.811857490738	0.325546066128	0.15755179288	0.877814804977	0.114801807676	0.478813657303	18.4033721363	-14.9295113262	69.6708181387
21	1.28468841293	0.195722481252	-2.68577639115	3.874620802	-1.42545361583	7.51448931781	-0.739103751717	-1.33675757332	0.506529212323	1.16871354999	0.628393006671	-1.18069956892	0.44810511047	0.822130646453	0.156280989266	0.969330401976	0.293033072216	-0.169092034665	0.645824001441	-0.1781597047	0.695857262517	30.9379778055	-27.4236087048	30.149696342
22	6.57533626473	-0.247186822228	-3.17011526784	3.3120276635	-1.46115249696	3.18029630009	-0.430377848528	0.946613879947	0.0815549836627	0.272222111322	0.543101795337	1.66304717884	-0.553390892714	-2.44869113042	-0.336833009462	0.760296994324	0.107147822514	0.0248911355647	1.01065158963	0.0609472906059	0.796593860259	9.70493252812	2.70854595898	7.30175782097
23	8.89687164002	1.03200275551	-5.81181299013	8.28726455325	-0.672807583823	9.20052060672	0.610719476299	1.4944765615	2.03992543695	-0.968909856041	-0.466965695859	-0.325956908393	-1.45138162505	0.359800989429	-0.226030133124	0.803207775657	0.0884074665397	-0.0488234698235	0.717110179025	0.138809877975	0.797638773843	-5.83042108063	7.81019319777	33.9757551297
24	2.44802939213	-0.954224047703	1.53427727383	2.71812582873	0.877034935137	3.13564009615	-0.371965891722	-0.617308127244	-1.06121075574	0.810445508869	0.548741151447	0.469023791782	1.4387814956	0.635478305552	-0.202971958496	1.20000098192	0.290865027457	0.138924573897	0.992217341602	0.0678685246632	1.06364506207	15.0516586322	-15.9206674148	53.5291101602

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 13 )	A	A	1 - 13	1 - 13
2	2	chain 'A' and (resid 14 through 28 )	A	A	14 - 28	14 - 28
3	3	chain 'A' and (resid 29 through 40 )	A	A	29 - 40	29 - 40
4	4	chain 'A' and (resid 41 through 56 )	A	A	41 - 56	41 - 56
5	5	chain 'A' and (resid 57 through 77 )	A	A	57 - 77	57 - 77
6	6	chain 'A' and (resid 78 through 92 )	A	A	78 - 92	78 - 92
7	7	chain 'A' and (resid 93 through 115 )	A	A	93 - 115	93 - 115
8	8	chain 'A' and (resid 116 through 138 )	A	A	116 - 138	116 - 138
9	9	chain 'A' and (resid 139 through 156 )	A	A	139 - 156	139 - 156
10	10	chain 'A' and (resid 157 through 170 )	A	A	157 - 170	157 - 170
11	11	chain 'A' and (resid 171 through 183 )	A	A	171 - 183	171 - 183
12	12	chain 'A' and (resid 184 through 206 )	A	A	184 - 206	184 - 206
13	13	chain 'A' and (resid 207 through 217 )	A	A	207 - 217	207 - 217
14	14	chain 'B' and (resid 2 through 92 )	B	B	2 - 92	1 - 91
15	15	chain 'B' and (resid 93 through 217 )	B	B	93 - 217	92 - 216
16	16	chain 'C' and (resid 1 through 92 )	C	C	1 - 92	1 - 92
17	17	chain 'C' and (resid 93 through 217 )	C	C	93 - 217	93 - 217
18	18	chain 'D' and (resid 2 through 77 )	D	D	2 - 77	1 - 68
19	19	chain 'D' and (resid 78 through 163 )	D	D	78 - 163	69 - 153
20	20	chain 'D' and (resid 164 through 215 )	D	D	164 - 215	154 - 203
21	21	chain 'E' and (resid 1 through 6 )	E	E	1 - 6
22	22	chain 'F' and (resid 1 through 5 )	F	F	1 - 5
23	23	chain 'G' and (resid 1 through 4 )	G	G	1 - 4
24	24	chain 'H' and (resid 1 through 3 )	H	H	1 - 3

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