PDB-5lut: Structures of DHBN domain of Gallus gallus BLM helicase

ID or keywords:

Entry

Database: PDB / ID: 5lut

Title

Structures of DHBN domain of Gallus gallus BLM helicase

Components

BLM helicase

Keywords

TRANSFERASE / helicase dimerization alpha-helix motif

Function / homology

Function and homology information

regulation of DNA-templated DNA replication / : / : / : / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA double-strand break processing / DNA clamp loader activity ...
Similarity search - Function

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.72 Å

Authors

Shi, J. / Chen, W.-F. / Zhang, B. / Fan, S.-H. / Ai, X. / Liu, N.-N. / Rety, S. / Xi, X.-G.

Citation

Journal: J. Biol. Chem. / Year: 2017
Title: A helical bundle in the N-terminal domain of the BLM helicase mediates dimer and potentially hexamer formation.
Authors: Shi, J. / Chen, W.F. / Zhang, B. / Fan, S.H. / Ai, X. / Liu, N.N. / Rety, S. / Xi, X.G.

History

Deposition	Sep 9, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 1, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 8, 2017	Group: Database references
Revision 1.2	Apr 19, 2017	Group: Database references
Revision 1.3	Nov 20, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5lut.cif.gz	221.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5lut.ent.gz	182.5 KB	Display	PDB format
PDBx/mmJSON format	5lut.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/lu/5lut ftp://data.pdbj.org/pub/pdb/validation_reports/lu/5lut	HTTPS FTP

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Related structure data

Related structure data	5lupC 5lusC 5mk5C C: citing same article (ref.)
Similar structure data	5jhc-2 1g3v-2 3kur-1 3kur-8 3kur-5 446d-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5lupC

5lusC

5mk5C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#255 - Mar 2021 Cisplatin and DNA similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: BLM helicase

B: BLM helicase

C: BLM helicase

D: BLM helicase

E: BLM helicase

F: BLM helicase

G: BLM helicase

H: BLM helicase

I: BLM helicase

J: BLM helicase

K: BLM helicase

hetero molecules

85.2 kDa, 11 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

K: BLM helicase

J: BLM helicase

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

2

A: BLM helicase

B: BLM helicase

hetero molecules

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

3

C: BLM helicase

D: BLM helicase

hetero molecules

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

4

E: BLM helicase

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

5

F: BLM helicase

G: BLM helicase

hetero molecules

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

6

H: BLM helicase

I: BLM helicase

hetero molecules

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

7

J: BLM helicase

K: BLM helicase

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

Unit cell

Length a, b, c (Å)	76.686, 230.804, 50.916
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	BLM helicase Mass: 7714.577 Da / Num. of mol.: 11 / Fragment: UNP residues 97-612 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: RCJMB04_17c23 / Plasmid: pET15b-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZJM1, UniProt: Q9I920*PLUS
#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.: 41 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.76 Å³/Da / Density % sol: 55.48 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 0.1M MgCl2 0.1M Na-Citrate 12% PEG 1500 15% Glycerol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9754 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9754 Å / Relative weight: 1
Reflection	Resolution: 2.718→54.302 Å / Num. obs: 25224 / % possible obs: 100 % / Redundancy: 11.6 % / B_iso Wilson estimate: 75.83 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.1144 / Net I/σ(I): 18.48
Reflection shell	Highest resolution: 2.815 Å / Redundancy: 12.5 % / R_merge(I) obs: 1.8552 / Mean I/σ(I) obs: 2.23 / CC_1/2: 0.802 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2650: ???)	refinement
XDS		data reduction
XDS		data scaling
autoSHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.72→72.774 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2829	1234	4.96 %	5%
R_work	0.2364	-	-	-
obs	0.2387	24904	98.82 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.72→72.774 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4052	0	20	41	4113

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4093
X-RAY DIFFRACTION	f_angle_d	1.119	5516
X-RAY DIFFRACTION	f_dihedral_angle_d	3.283	2588
X-RAY DIFFRACTION	f_chiral_restr	0.051	682
X-RAY DIFFRACTION	f_plane_restr	0.006	699

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 (%)
2.7201-2.829	0.3847	149	0.3689	2421	X-RAY DIFFRACTION	93
2.829-2.9577	0.392	131	0.3363	2533	X-RAY DIFFRACTION	97
2.9577-3.1137	0.374	130	0.2933	2585	X-RAY DIFFRACTION	100
3.1137-3.3088	0.3201	122	0.2828	2642	X-RAY DIFFRACTION	100
3.3088-3.5642	0.3401	140	0.272	2622	X-RAY DIFFRACTION	100
3.5642-3.9229	0.2802	151	0.2294	2642	X-RAY DIFFRACTION	100
3.9229-4.4905	0.244	140	0.1846	2649	X-RAY DIFFRACTION	100
4.4905-5.6572	0.2598	131	0.2244	2731	X-RAY DIFFRACTION	100
5.6572-72.8002	0.2445	140	0.2178	2845	X-RAY DIFFRACTION	100

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	3.933	-0.6466	0.1869	4.5169	-0.4328	4.3044	-0.0693	0.0888	0.388	-0.3445	0.2937	0.1442	0.1877	0.2893	-0.1447	0.3789	0.0261	-0.0097	0.3859	0.0195	0.4877	-38.9258	47.5926	42.6193
2	6.6993	3.1205	-2.3946	4.2913	-0.6344	4.1171	0.3617	-0.6403	0.2386	0.5955	-0.269	-0.6987	-0.2797	0.6494	-0.0178	0.3324	0.0922	-0.0604	0.506	-0.0182	0.4818	-28.7069	51.3809	48.479
3	4.4427	1.189	-1.6182	2.2125	-0.6884	2.3185	0.2771	0.9152	0.2744	0.0064	0.1283	-0.7417	-0.2119	0.2655	-0.193	0.4542	0.109	0.0766	0.6147	0.0116	0.6449	-28.6312	44.1238	41.3814
4	1.6176	-0.5057	-0.6394	2.8106	0.6994	3.3364	-0.141	0.1109	-0.0198	-0.138	0.1184	0.3132	0.2116	-0.5145	-0.1058	0.5141	0.0134	-0.104	0.4179	0.1042	0.4771	-45.676	41.2217	42.1181
5	5.0859	-2.5781	-0.2382	4.2699	0.3014	2.4973	-0.1914	-0.3767	-0.3835	-0.5054	0.4166	-0.7853	0.1147	0.5909	-0.1615	0.6024	-0.0891	0.1205	0.6307	-0.0138	0.6229	-32.9441	23.8205	35.4226
6	5.5296	3.0074	-1.4939	8.4797	-0.8833	4.276	-0.3743	-0.138	0.4183	-0.5194	0.2756	1.5367	-0.5294	-1.486	0.28	0.5387	0.1474	-0.1237	0.6693	0.0331	0.5492	-54.8634	27.0228	37.4151
7	4.828	1.5814	1.2144	4.6301	0.8173	3.5923	-0.0539	-0.1024	0.0838	0.5732	0.0248	-0.2031	-0.1035	-0.2651	-0.0283	0.5452	0.0908	0.0073	0.5205	0.0518	0.4556	-41.7034	29.335	47.4471
8	4.1363	-0.6436	1.2626	4.0728	0.1534	3.9691	-0.2324	-0.3514	-0.5322	0.477	0.0087	-0.599	0.0504	0.8298	0.1716	0.5521	0.0534	0.0034	0.6224	0.0872	0.4686	-35.2387	21.7472	45.9141
9	1.8972	-2.8186	1.3668	6.7599	0.9027	4.3467	0.607	0.5165	-0.2473	-0.3877	-0.8019	0.656	0.3337	-1.0751	-0.0508	0.5793	-0.0319	-0.093	0.5749	0.0044	0.5219	-53.1512	21.6977	30.6097
10	4.112	-0.9545	0.2597	3.6692	0.2855	2.5898	-0.073	0.6052	-0.0366	-0.8083	0.003	-0.5988	0.4096	0.0118	0.1039	0.6545	-0.0771	0.1417	0.4406	-0.0148	0.5247	-37.3949	16.7201	29.6897
11	3.9074	-0.9637	1.415	4.7272	-0.761	4.6257	0.104	-0.8048	0.3552	0.5746	-0.0123	-0.7386	-0.5885	-0.2145	-0.151	0.508	-0.0461	-0.0434	0.5416	-0.0953	0.6734	-33.3959	1.0033	41.1258
12	4.604	-0.2587	0.2282	5.2094	0.3959	3.9474	0.3985	0.9099	-0.0066	-0.7136	-0.0844	0.5231	-0.2361	-0.114	-0.064	0.5113	0.0068	-0.0325	0.5225	0.1135	0.5214	-45.2538	5.618	31.082
13	4.4012	0.3351	0.2522	3.8037	-1.3475	5.6189	0.002	0.8426	0.1271	-1.244	-0.0181	-0.3171	0.4687	0.3519	-0.2233	0.6565	-0.0122	0.0042	0.5494	0.0035	0.5115	-29.5006	66.952	33.5703
14	3.1314	1.5495	1.212	3.9186	0.3333	3.9576	0.2403	-0.6228	-0.2109	0.5266	-0.3072	0.3412	0.1166	-0.2996	-0.0116	0.3527	0.0673	0.0932	0.5079	0.0625	0.5014	-34.9203	63.8001	50.9102
15	4.0293	2.0663	1.7163	4.1987	0.7962	4.7644	-0.52	0.3218	0.6027	-0.4601	0.1705	1.2735	-0.1788	-0.2568	0.2801	0.386	0.1044	-0.0541	0.4334	0.0148	0.6238	-38.0068	69.8642	40.6239
16	3.1691	-1.2871	-0.612	3.1322	-0.5614	3.8752	0.1353	0.0384	-0.0582	-0.269	0.0594	-0.0476	-0.1716	0.384	-0.0798	0.4419	-0.0642	0.0733	0.416	-0.1191	0.3882	-21.8379	72.7369	42.7162
17	4.5176	-1.207	1.032	3.9429	0.2709	2.909	0.6943	0.6062	0.4279	-0.2852	0.0769	1.6356	-0.6346	-1.8909	-0.6007	0.5681	0.1262	-0.0058	1.064	0.1704	0.9525	-34.1101	88.0564	33.6481
18	4.4533	3.1736	0.5574	5.1129	-2.4256	6.1304	-0.0784	-0.6811	-0.3847	1.2418	-0.2053	-0.8385	-0.5885	1.2422	0.1805	0.6574	0.0921	0.0822	0.6691	-0.0578	0.5746	-13.7787	89.0048	38.9668
19	5.7043	-0.289	-1.1849	3.8275	-1.2713	7.285	0.8015	-0.6661	-0.0876	0.3507	-0.333	0.7839	-1.6616	0.3916	-0.1909	0.635	0.0586	0.1007	0.3753	-0.0703	0.4837	-28.2619	84.5383	46.9606
20	3.3578	0.3708	-1.1623	1.9124	-0.3867	3.6651	0.2624	0.1514	0.8401	1.2116	0.493	0.8751	-0.9635	-1.4262	-0.8097	0.8724	0.1631	0.3368	0.6652	0.0542	0.8463	-33.155	92.2664	43.1503
21	1.9335	-2.2568	0.4554	6.8595	1.0436	2.8473	0.3142	-0.8185	0.5417	0.899	-0.0889	0.2393	-0.6679	0.8345	-0.3111	0.7163	-0.0449	0.1011	0.5934	-0.0922	0.5578	-15.2496	93.2371	30.6995
22	4.0657	0.5795	3.0016	4.839	3.1418	3.8281	0.7986	2.0033	0.2765	-1.1747	1.6229	0.2569	-0.2225	-1.3136	-0.3159	0.6444	0.0721	0.0783	0.7867	0.6278	0.5854	-28.3918	94.1467	27.3963
23	3.3753	2.6857	-1.2279	2.51	-1.2427	0.6236	-0.3213	0.6117	0.1379	-1.4251	0.6477	-0.0891	0.8616	-1.6404	-0.0158	1.6176	0.1236	-0.1137	1.3436	0.3646	1.0701	-37.2792	108.202	30.2537
24	2.08	-0.8439	0.1513	1.3451	1.7283	4.6186	-1.0419	0.9899	1.2229	-1.362	-0.9654	-0.2654	0.0291	-0.2371	1.0367	1.5374	0.338	0.0703	1.9612	0.0651	1.0978	-28.4163	105.8134	18.3812
25	1.3294	-0.6735	-0.6127	2.5139	-1.696	2.1481	-0.3997	-1.743	-0.7737	-0.1104	-0.3861	0.1395	-0.354	-0.4684	0.5504	2.0032	0.1213	-0.1867	4.034	0.3078	0.863	-24.6361	112.2145	25.4802
26	0.2119	0.2042	-0.274	0.2665	-0.2185	0.3813	0.1438	-0.0893	-0.433	-0.2909	-0.0794	-0.2107	-0.0548	-0.1062	0.0442	3.4634	1.0028	-0.5127	0.9284	-1.6296	0.732	-25.9258	103.6964	39.7536
27	7.442	-0.4655	-0.0626	7.4422	-1.1258	0.1696	-0.9028	-0.495	-1.3725	-0.7743	0.5222	-0.2938	-0.5518	-0.9801	0.22	1.9254	0.03	0.0327	1.7161	-0.0084	0.8746	-47.8233	117.5882	42.6632
28	3.6164	-0.5695	0.5963	4.8857	-2.2325	1.2543	-0.0531	-0.5309	1.3826	0.1422	-0.125	0.0856	-0.1404	0.4579	0.1341	0.4985	-0.2265	-0.3459	1.3719	0.2123	1.3516	-43.0287	112.6854	26.2705

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 310 through 341 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 342 through 361 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 309 through 330 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 331 through 361 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 310 through 330 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 331 through 341 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 342 through 361 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 308 through 330 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 331 through 341 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 342 through 361 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 310 through 330 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 331 through 361 )
13	X-RAY DIFFRACTION	13	chain 'F' and (resid 307 through 330 )
14	X-RAY DIFFRACTION	14	chain 'F' and (resid 331 through 361 )
15	X-RAY DIFFRACTION	15	chain 'G' and (resid 310 through 330 )
16	X-RAY DIFFRACTION	16	chain 'G' and (resid 331 through 361 )
17	X-RAY DIFFRACTION	17	chain 'H' and (resid 312 through 330 )
18	X-RAY DIFFRACTION	18	chain 'H' and (resid 331 through 343 )
19	X-RAY DIFFRACTION	19	chain 'H' and (resid 344 through 361 )
20	X-RAY DIFFRACTION	20	chain 'I' and (resid 310 through 330 )
21	X-RAY DIFFRACTION	21	chain 'I' and (resid 331 through 341 )
22	X-RAY DIFFRACTION	22	chain 'I' and (resid 342 through 357 )
23	X-RAY DIFFRACTION	23	chain 'J' and (resid 320 through 328 )
24	X-RAY DIFFRACTION	24	chain 'J' and (resid 329 through 338 )
25	X-RAY DIFFRACTION	25	chain 'J' and (resid 339 through 351 )
26	X-RAY DIFFRACTION	26	chain 'J' and (resid 352 through 359 )
27	X-RAY DIFFRACTION	27	chain 'K' and (resid 311 through 320 )
28	X-RAY DIFFRACTION	28	chain 'K' and (resid 321 through 332 )

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi