PDB-9dbi: Structure of Hailong HalB D21A/D23A mutant

ID or keywords:

Entry

Database: PDB / ID: 9dbi

Title

Structure of Hailong HalB D21A/D23A mutant

Components

HalB

Keywords

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

Function / homology

PHOSPHATE ION

Function and homology information

Biological species

Rhodobacteraceae bacterium QY30 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.99 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: Nature / Year: 2025
Title: A DNA-gated molecular guard controls bacterial Hailong anti-phage defence.
Authors: Tan, J.M.J. / Melamed, S. / Cofsky, J.C. / Syangtan, D. / Hobbs, S.J. / Del Marmol, J. / Jost, M. / 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
Revision 1.1	May 14, 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	Jul 30, 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	9dbi.cif.gz	444.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9dbi.ent.gz	305.8 KB	Display	PDB format
PDBx/mmJSON format	9dbi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9dbi_validation.pdf.gz	462.2 KB	Display	wwPDB validaton report
Full document	9dbi_full_validation.pdf.gz	470.4 KB	Display
Data in XML	9dbi_validation.xml.gz	45.9 KB	Display
Data in CIF	9dbi_validation.cif.gz	60.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/db/9dbi ftp://data.pdbj.org/pub/pdb/validation_reports/db/9dbi	HTTPS FTP

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Related structure data

Related structure data	9dbjC C: citing same article (ref.)
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

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	71.807, 122.287, 141.010
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	HalB Mass: 25853.322 Da / Num. of mol.: 4 / Mutation: D21A,D23A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacteraceae bacterium QY30 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 600 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.99 Å³/Da / Density % sol: 58.91 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.0, 5% PEG-4000

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 10, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.99→71.81 Å / Num. obs: 85256 / % possible obs: 99.3 % / Redundancy: 14.3 % / B_iso Wilson estimate: 35.8 Å² / R_pim(I) all: 0.053 / Net I/σ(I): 9.4
Reflection shell	Resolution: 1.99→2.02 Å / Num. unique obs: 4180 / R_pim(I) all: 0.856

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
xia2.multiplex		data reduction
xia2.multiplex		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.99→70.51 Å / SU ML: 0.2558 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9439
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2201	1985	2.33 %
R_work	0.1852	83171	-
obs	0.186	85156	99.21 %

Solvent computation

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

Displacement parameters

B_iso mean: 49.05 Å²

Refinement step

Cycle: LAST / Resolution: 1.99→70.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6976	0	20	600	7596

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0071	7107
X-RAY DIFFRACTION	f_angle_d	0.791	9553
X-RAY DIFFRACTION	f_chiral_restr	0.0466	1062
X-RAY DIFFRACTION	f_plane_restr	0.0086	1221
X-RAY DIFFRACTION	f_dihedral_angle_d	12.9879	2650

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 (%)
1.99-2.04	0.3682	128	0.3284	5858	X-RAY DIFFRACTION	98.39
2.04-2.09	0.3106	137	0.2928	5814	X-RAY DIFFRACTION	98.64
2.09-2.16	0.3133	131	0.2564	5852	X-RAY DIFFRACTION	98.78
2.16-2.23	0.2526	138	0.2325	5855	X-RAY DIFFRACTION	98.76
2.23-2.31	0.2511	174	0.2207	5831	X-RAY DIFFRACTION	98.9
2.31-2.4	0.2429	136	0.2116	5907	X-RAY DIFFRACTION	99.08
2.4-2.51	0.2356	149	0.1922	5872	X-RAY DIFFRACTION	99.23
2.51-2.64	0.2242	144	0.1864	5899	X-RAY DIFFRACTION	99.26
2.64-2.8	0.2166	149	0.178	5911	X-RAY DIFFRACTION	99.41
2.8-3.02	0.2362	152	0.1812	5944	X-RAY DIFFRACTION	99.43
3.02-3.33	0.2421	138	0.1787	5988	X-RAY DIFFRACTION	99.64
3.33-3.81	0.2208	146	0.1636	6030	X-RAY DIFFRACTION	99.71
3.81-4.8	0.1653	129	0.1493	6100	X-RAY DIFFRACTION	99.87
4.8-70.51	0.1854	134	0.1818	6310	X-RAY DIFFRACTION	99.74

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	1.84657860363	-0.302463073233	-1.21028579848	7.19515013714	-1.15748965649	6.02602303836	-0.205275083396	-0.654624551112	0.185555813913	1.21218317319	0.207041789359	0.100557978036	0.0451827973324	0.0105817087428	0.00290763158829	0.476743186207	-0.032409131153	0.0410873611936	0.305172241808	-0.00817743699564	0.300160860519	-22.684936137	7.8745405949	65.2215371435
2	2.68957668223	0.613604941453	0.377689245894	3.73069226795	1.22490590012	2.41262287737	0.00790422263205	-0.373487743535	0.144099139364	0.227330379013	-0.00309362929389	-0.0148963073598	-0.0664102376688	0.0228433522785	0.0678793245801	0.237506530051	-0.000138588239332	0.0395964282242	0.243618956202	0.00868957829401	0.227662668222	-18.5084869126	20.1874892163	63.3667387368
3	4.25449485481	0.104749298666	1.06114235748	3.92750146353	1.81212962372	6.75792595465	0.0698995568557	-0.330382734048	0.0517131424294	0.371919966259	0.188430138356	-0.615372940595	0.310211010196	0.770342793087	-0.127616918979	0.317950484984	0.00160071354601	-0.0347942735475	0.376101593044	-0.0201300316256	0.391018009387	-4.77222229091	20.6804599805	64.4778388353
4	4.53358601858	-1.5946724639	-1.06196836703	4.75999237789	1.40378331954	6.38488686853	-0.318122024075	-0.580783887426	0.0901129246143	0.568098520958	0.361287252155	-0.240810121012	0.093546375903	0.0959504649529	0.0124568411028	0.465987161376	-0.00728187376815	-0.0813105040035	0.484139250452	-0.0245337711357	0.344121894478	-10.7629827176	27.7579352262	75.8194847626
5	3.10182135501	-0.553496445982	0.562730353448	5.80377730161	0.04951650654	3.41884728587	-0.149239036884	-0.348568882449	0.180177687299	0.763656147186	0.0889577973235	0.171932663843	-0.351938398958	0.0624239115683	0.0840173634552	0.326877888428	0.0114459608456	0.0230255399274	0.209849627248	0.0192510256847	0.210792812236	-19.5106259297	-10.5121582498	63.5338073378
6	3.5265970077	1.04909731523	-1.90419020237	1.0392630805	-1.14213810011	2.2979320124	0.121065475714	-0.228321090051	0.134091822165	0.0868527574601	-0.0471011422253	0.0510822140703	0.0847975980216	0.0758691645525	-0.0978522495752	0.226879211849	-0.00497593279917	-0.0117421140423	0.19851529721	-0.00740810976393	0.213845579565	-29.6520786049	-23.9291809059	65.3351156899
7	5.06789302439	-0.0717485288902	1.00600049779	2.59446061423	-1.00668831454	6.61640300773	-0.0244247131274	-0.142806906464	0.283114976691	0.174447086858	0.0560169860383	0.0520883755517	-0.382471554096	-0.119767487376	-0.0276422623108	0.285381324331	-0.0291126636627	0.0516295448145	0.231441702702	-0.0173075559744	0.264385331019	-37.0283947203	-26.8613152258	73.286192258
8	2.52103303629	0.832869164341	0.745868352237	6.0986856124	-0.138341725838	3.31807343365	-0.15292823082	0.367870852437	0.137091256176	-0.581778491153	0.0628539713085	-0.0228633706273	-0.277686481769	0.0881187346021	0.0841383497664	0.314900556526	0.00417083485613	0.0224106687992	0.254414853259	0.0478506925808	0.237421597264	-21.2957180083	-11.318508206	37.9961679508
9	3.21412861131	-1.24007888716	-1.3229504699	2.23469898709	0.836318081614	2.85306970524	0.203320062037	0.22958371536	0.0610669627945	-0.303250199032	-0.125423907279	-0.260016381027	0.075593410832	0.358334261781	-0.0748245913716	0.270088835466	0.0571697732026	0.00177800749244	0.258499425952	0.0410216871557	0.228235399941	-7.94874617741	-26.7742634843	36.8107414187
10	3.70778860867	0.872055527113	1.07551579802	2.16290264087	0.698512421047	6.8075887738	0.0665666528659	0.4734477804	-0.146249063403	-0.318779993985	0.0494770995531	0.169756398101	0.198156828196	-0.197961944487	-0.110758509811	0.479116513705	0.0674812413118	-0.0354997980554	0.465331463051	-0.0136512050995	0.280976907998	-12.370000316	-32.2728429339	24.8068240272
11	3.53283566072	0.946000133185	-0.40717622463	7.07121835899	0.471182154156	6.58472991329	-0.163142857478	0.591350124494	0.0705279023874	-1.01251837273	0.109624917464	0.0164802867864	0.203210985616	0.149236460152	0.0623067178385	0.422109054776	0.0185859153218	-0.00147832300664	0.24426978961	0.061221832779	0.283437090278	-15.9766944808	6.39233406514	35.4802405576
12	2.39234530448	-1.74431520208	1.65300929445	1.583996272	-1.44198306712	2.44420191691	0.0693442817794	0.0770657827755	0.0482533946888	-0.148120589103	-0.0976754410112	-0.0785081485569	0.0270123743539	0.106756600011	0.0403115234643	0.268734471781	-0.0172438031974	0.0226487240438	0.224135363339	0.035958512711	0.312385237338	-22.492226166	19.1604516076	36.2702920007
13	5.93312443465	-0.875084272427	-1.01583635924	3.02611392109	-0.652124632461	6.59505203373	-0.0555168871151	0.214595839115	-0.324669434916	-0.075042585015	-0.132996775535	-0.0479867183459	0.19858663769	0.240739489852	0.118200918809	0.337439307939	0.0252955206435	-0.0413741324191	0.214281949951	0.0132135098156	0.316187850661	-29.5472059478	24.5989069608	24.9065515751

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 0 through 56 )	A	A	0 - 56	1 - 56
2	2	chain 'A' and (resid 57 through 115 )	A	A	57 - 115	57 - 115
3	3	chain 'A' and (resid 116 through 169 )	A	A	116 - 169	116 - 168
4	4	chain 'A' and (resid 170 through 227 )	A	A	170 - 227	169 - 222
5	5	chain 'B' and (resid 1 through 77 )	B	B	1 - 77	1 - 75
6	6	chain 'B' and (resid 78 through 151 )	B	B	78 - 151	76 - 149
7	7	chain 'B' and (resid 152 through 227 )	B	B	152 - 227	150 - 216
8	8	chain 'C' and (resid 1 through 77 )	C	C	1 - 77	1 - 76
9	9	chain 'C' and (resid 78 through 183 )	C	C	78 - 183	77 - 181
10	10	chain 'C' and (resid 184 through 227 )	C	C	184 - 227	182 - 220
11	11	chain 'D' and (resid 1 through 56 )	D	D	1 - 56	1 - 55
12	12	chain 'D' and (resid 57 through 151 )	D	D	57 - 151	56 - 150
13	13	chain 'D' and (resid 152 through 227 )	D	D	152 - 227	151 - 217

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