PDB-8bdk: Structure of a non-canonical histone from archaea

ID or keywords:

Entry

Database: PDB / ID: 8bdk

Title

Structure of a non-canonical histone from archaea

Components

DNA-binding protein HmvA

Keywords

DNA BINDING PROTEIN / histone / dimerisation / transcription

Function / homology

: / Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / Histone-fold / chromosome / protein heterodimerization activity / DNA binding / cytoplasm / DNA-binding protein HmvA

Function and homology information

Biological species

Methanocaldococcus jannaschii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.88 Å

Authors

Ofer, S. / Werner, F.

Funding support

1items

Citation

Journal: Commun Biol / Year: 2023
Title: DNA-bridging by an archaeal histone variant via a unique tetramerisation interface.
Authors: Ofer, S. / Blombach, F. / Erkelens, A.M. / Barker, D. / Soloviev, Z. / Schwab, S. / Smollett, K. / Matelska, D. / Fouqueau, T. / van der Vis, N. / Kent, N.A. / Thalassinos, K. / Dame, R.T. / Werner, F.

History

Deposition	Oct 19, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 12, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Feb 7, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8bdk.cif.gz	173.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8bdk.ent.gz	140.8 KB	Display	PDB format
PDBx/mmJSON format	8bdk.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/bd/8bdk ftp://data.pdbj.org/pub/pdb/validation_reports/bd/8bdk	HTTPS FTP

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Related structure data

Related structure data	1b67S S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#7 - Jul 2000 Nucleosome similarity (1) #67 - Jul 2005 TATA-Binding Protein similarity (2)

Deposited unit

A: DNA-binding protein HmvA

B: DNA-binding protein HmvA

D: DNA-binding protein HmvA

E: DNA-binding protein HmvA

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

1

A: DNA-binding protein HmvA

B: DNA-binding protein HmvA

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

2

D: DNA-binding protein HmvA

E: DNA-binding protein HmvA

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

Unit cell

Length a, b, c (Å)	42.016, 81.154, 53.543
Angle α, β, γ (deg.)	90.000, 98.710, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	DNA-binding protein HmvA Mass: 11221.226 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: hmvA, MJ1647 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59041
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.01 Å³/Da / Density % sol: 38.81 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M NaOAc pH 4.6, 10% (w/v) PEG 3350 and 5% (w/v) tacsimate pH 4.6

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 8, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.88→80 Å / Num. obs: 28933 / % possible obs: 100 % / Redundancy: 3.3 % / CC_1/2: 0.9958 / R_merge(I) obs: 0.099 / R_pim(I) all: 0.053 / Net I/σ(I): 7.3
Reflection shell	Resolution: 1.88→1.91 Å / Num. unique obs: 1466 / CC_1/2: 0.517 / R_pim(I) all: 0.67

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
PDB_EXTRACT	3.27	data extraction
xia2		data reduction
pointless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1B67

1b67

Resolution: 1.88→52.925 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2529	1405	4.92 %
R_work	0.2078	27173	-
obs	0.21	28578	98.73 %

Solvent computation

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

Displacement parameters

B_iso max: 113.97 Å² / B_iso mean: 38.5749 Å² / B_iso min: 11.54 Å²

Refinement step

Cycle: final / Resolution: 1.88→52.925 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3092	0	0	240	3332
B_iso mean	-	-	-	39.4	-
Num. residues	-	-	-	-	384

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3131
X-RAY DIFFRACTION	f_angle_d	0.764	4178
X-RAY DIFFRACTION	f_chiral_restr	0.043	503
X-RAY DIFFRACTION	f_plane_restr	0.004	528
X-RAY DIFFRACTION	f_dihedral_angle_d	12.411	2081

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.88-1.9472	0.4082	139	0.3665	2626	96
1.9472-2.0252	0.3958	147	0.318	2666	98
2.0252-2.1174	0.3173	143	0.2802	2692	99
2.1174-2.229	0.3141	126	0.254	2728	99
2.229-2.3686	0.2794	154	0.2262	2694	99
2.3686-2.5515	0.3011	133	0.212	2732	99
2.5515-2.8083	0.2525	142	0.2038	2750	99
2.8083-3.2146	0.2572	145	0.2006	2722	100
3.2146-4.0498	0.1899	142	0.164	2763	100
4.0498-52.925	0.2012	134	0.1748	2800	99

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	3.9945	1.6072	1.5566	6.4654	3.0572	5.0457	-0.0214	-0.3645	0.0776	0.4348	-0.2247	0.7397	-0.1646	-0.6536	0.2613	0.3102	0.0646	0.0895	0.2746	-0.0539	0.2931	12.3385	34.2783	106.5636
2	1.3567	-1.483	-0.8764	8.292	4.381	3.0434	0.2175	0.1821	0.1235	-0.6827	-0.38	-0.0391	-0.2343	-0.1673	0.1563	0.2598	0.0421	-0.0155	0.2201	0.018	0.1739	18.535	22.3058	92.9009
3	6.5269	0.7863	1.6935	9.1411	0.9759	7.9299	-0.0354	-0.2323	-0.0481	-0.1736	-0.1532	-0.0226	-0.4682	-0.1534	0.1905	0.2603	0.0263	-0.0172	0.1372	0.0037	0.1535	21.4023	7.5795	95.5228
4	7.721	5.9549	-1.2792	7.0892	1.9462	3.7397	0.2502	0.3951	0.4081	0.2068	-0.2918	-1.5814	1.0596	0.9492	0.0745	0.4248	0.1746	0.0207	0.4189	0.0492	0.6315	38.1672	18.1702	95.5559
5	2.3064	-1.3697	2.7315	5.4781	-0.9087	3.3351	-0.6254	0.4511	-0.6066	0.0629	-0.3617	-1.2763	0.033	0.5633	0.9265	0.6151	0.162	0.1537	0.4165	0.1069	0.4547	32.629	28.922	87.1017
6	8.0558	-0.9288	3.5764	2.1669	0.0824	6.9989	0.003	-0.3454	0.6999	0.3058	0.0299	-0.4483	0.0905	0.0098	0.0049	0.2833	0.0331	-0.0216	0.2352	-0.0171	0.2986	28.2928	30.2856	98.8306
7	5.9142	-1.4763	-2.7724	7.2628	1.4694	5.0163	0.1039	-0.0222	0.3923	-0.3655	-0.3183	0.8419	-0.5125	-0.3711	0.111	0.2523	0.0525	-0.1214	0.2538	-0.0427	0.3794	9.6826	17.011	94.2009
8	2.6884	2.7085	1.3327	7.001	3.7871	3.2636	0.0998	-0.2868	-0.0096	0.6195	-0.2559	0.0821	0.0743	-0.1009	0.1525	0.2635	0.0432	-0.0156	0.2267	0.0036	0.1371	20.4807	30.3472	106.0345
9	2.3968	2.0431	-3.0521	8.6661	-3.6742	7.221	-0.6355	0.4219	-0.0043	-1.0742	0.064	-1.1981	-0.4193	1.137	0.7974	0.5271	-0.0573	-0.0279	0.4429	-0.0465	0.3965	27.6025	39.8668	98.1483
10	2.4942	-0.5493	-4.0287	2.1754	1.8545	9.7382	0.175	-0.7106	2.2208	0.0718	-0.0732	-1.2913	-1.1913	1.5305	-0.0802	0.317	0.0274	-0.1186	0.6365	0.0497	1.4065	39.0533	29.402	98.7477
11	9.3405	1.8744	-1.0451	2.7194	1.8607	8.1862	-0.1422	-0.3269	-0.2255	-0.0108	0.2127	-0.3822	0.3481	0.6565	-0.0736	0.2711	0.0521	-0.0004	0.2003	0.0238	0.2877	28.995	19.0274	100.0278
12	2.0634	2.4533	-0.5853	8.5634	-2.5131	1.7302	0.0428	-0.1428	-0.0526	0.4074	-0.1917	-0.3715	-0.0919	0.0845	0.1271	0.2092	0.0189	0.0301	0.1959	0.0059	0.1678	39.6163	14.632	78.4366
13	6.5917	3.0532	-0.602	6.9853	1.4112	8.0537	-0.2669	1.1624	0.6986	-1.0622	-0.165	1.2041	-0.0238	-0.7654	-0.0521	0.4244	0.0086	-0.0231	0.4027	0.0138	0.3849	30.2871	0.6228	71.4368
14	2.7797	1.819	1.5073	6.249	1.1114	5.9348	0.0902	0.1589	-0.3463	0.0587	-0.2538	0.888	0.2424	-1.165	0.0993	0.2472	-0.0368	0.0164	0.375	-0.0905	0.4638	23.9598	16.9598	70.6672
15	9.6493	2.7491	-0.2778	9.4114	1.1838	2.6988	-0.1071	-0.4209	-0.0416	0.3043	-0.0447	-0.231	0.1259	0.2959	0.2289	0.3181	0.0285	-0.0488	0.1952	0.03	0.1669	42.02	6.079	84.175
16	0.3654	-0.4493	0.8808	4.6821	-5.4523	6.3275	0.1399	0.0587	-0.0432	-0.8603	-0.2697	0.0109	0.3992	0.2421	0.2015	0.1751	0.018	0.0391	0.211	-0.002	0.1745	40.6912	18.1304	69.2425
17	5.0273	-1.1238	-1.4979	7.7877	-0.8254	8.0236	0.1127	-0.1787	-0.0286	0.2579	-0.2259	0.1199	-0.4281	-0.0518	0.0458	0.2628	0.0175	0.0475	0.1736	0.0131	0.2029	37.2022	32.872	70.7677
18	6.9214	-1.8697	-1.2899	4.2965	-0.5896	7.6441	0.325	1.3662	0.4858	-0.6327	-0.7942	0.9822	-1.3399	-0.8681	0.3685	0.4329	0.1795	-0.0858	0.473	-0.0879	0.5687	21.4356	22.6992	64.9676
19	7.9432	-2.1793	-3.0812	5.1267	-1.5497	2.4635	-0.6269	0.2029	0.4572	-0.7292	-0.2169	0.6414	0.0106	-0.4689	0.3922	0.4284	-0.0047	-0.0197	0.2959	-0.0386	0.3434	28.978	11.4578	59.1861
20	6.7598	-0.1354	-2.788	2.1495	-0.2519	6.4902	0.1192	-0.0761	-0.0432	-0.0457	0.1695	0.4488	0.4184	-0.3176	-0.2925	0.2931	0.0321	-0.0273	0.194	0.025	0.2941	29.4778	10.0339	71.873

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 20 )	A	1 - 20
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 49 )	A	21 - 49
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 50 through 63 )	A	50 - 63
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 64 through 76 )	A	64 - 76
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 77 through 82 )	A	77 - 82
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 83 through 96 )	A	83 - 96
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 20 )	B	1 - 20
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 21 through 55 )	B	21 - 55
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 56 through 63 )	B	56 - 63
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 64 through 77 )	B	64 - 77
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 78 through 96 )	B	78 - 96
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 1 through 55 )	D	1 - 55
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 56 through 63 )	D	56 - 63
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 64 through 96 )	D	64 - 96
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 1 through 20 )	E	1 - 20
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 21 through 49 )	E	21 - 49
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 50 through 63 )	E	50 - 63
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 64 through 76 )	E	64 - 76
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 77 through 82 )	E	77 - 82
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 83 through 96 )	E	83 - 96

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