PDB-5lus: Structures of DHBN domain of Pelecanus crispus BLM helicase

ID or keywords:

Entry

Database: PDB / ID: 5lus

Title

Structures of DHBN domain of Pelecanus crispus BLM helicase

Components

BLM helicase

Keywords

HYDROLASE / helicase dimerization alpha-helix motif

Function / homology

Function and homology information

hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / 3'-5' DNA helicase activity / DNA recombination /

DNA helicase /

DNA replication /

DNA repair /

DNA binding /

ATP binding /

nucleus
Similarity search - Function

Biological species

Pelecanus crispus (Dalmatian pelican)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.433 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	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5lus.cif.gz	308.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5lus.ent.gz	260.5 KB	Display	PDB format
PDBx/mmJSON format	5lus.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/5lus ftp://data.pdbj.org/pub/pdb/validation_reports/lu/5lus	HTTPS FTP

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Related structure data

Related structure data	5lupC 5lutC 5mk5C C: citing same article (ref.)
Similar structure data	5lup-1 5mk5-1 5mk5-2 2bp2-d 1zle-3 3k7c-4 2red-d 2jr7-d 5lut-6 2ril-d 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

5lutC

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

76.4 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: BLM helicase

B: BLM helicase

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

2

C: BLM helicase

D: BLM helicase

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

3

E: BLM helicase

F: BLM helicase

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

4

G: BLM helicase

H: BLM helicase

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

5

I: BLM helicase

J: BLM helicase

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

Unit cell

Length a, b, c (Å)	62.188, 72.408, 79.234
Angle α, β, γ (deg.)	90.00, 99.44, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	BLM helicase Mass: 7642.934 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pelecanus crispus (Dalmatian pelican) / Gene: N334_02369 / Plasmid: pET15b-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A091SV96
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.31 Å³/Da / Density % sol: 46.9 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.6 / Details: 0.2M NH4 Acetate 0.1M Na Citrate 16% PEG 3350

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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 7, 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: 1.433→36.2 Å / Num. obs: 105436 / % possible obs: 83 % / Redundancy: 3.2 % / B_iso Wilson estimate: 20.19 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.034 / Net I/σ(I): 18.56
Reflection shell	Highest resolution: 1.484 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.3467 / Mean I/σ(I) obs: 2.26 / CC_1/2: 0.802 / % possible all: 54

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.433→36.2 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.33

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1717	5242	4.97 %	5%
R_work	0.157	-	-	-
obs	0.1578	105370	82.91 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.433→36.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3918	0	0	661	4579

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3943
X-RAY DIFFRACTION	f_angle_d	1.239	5290
X-RAY DIFFRACTION	f_dihedral_angle_d	11.31	1558
X-RAY DIFFRACTION	f_chiral_restr	0.052	644
X-RAY DIFFRACTION	f_plane_restr	0.005	668

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 (%)
1.4331-1.4494	0.2643	103	0.2436	1984	X-RAY DIFFRACTION	49
1.4494-1.4664	0.2601	115	0.2224	2173	X-RAY DIFFRACTION	54
1.4664-1.4843	0.2463	125	0.2142	2286	X-RAY DIFFRACTION	58
1.4843-1.5031	0.2351	143	0.1923	2543	X-RAY DIFFRACTION	64
1.5031-1.5229	0.2163	151	0.1947	2732	X-RAY DIFFRACTION	68
1.5229-1.5438	0.192	144	0.1848	3010	X-RAY DIFFRACTION	74
1.5438-1.5658	0.1832	151	0.1725	3269	X-RAY DIFFRACTION	81
1.5658-1.5892	0.2171	193	0.1617	3536	X-RAY DIFFRACTION	88
1.5892-1.614	0.1577	191	0.1621	3922	X-RAY DIFFRACTION	98
1.614-1.6405	0.1678	209	0.1553	3979	X-RAY DIFFRACTION	99
1.6405-1.6688	0.1706	224	0.1578	3930	X-RAY DIFFRACTION	99
1.6688-1.6991	0.1789	240	0.1624	3959	X-RAY DIFFRACTION	99
1.6991-1.7318	0.2113	117	0.155	2560	X-RAY DIFFRACTION	64
1.7318-1.7671	0.1845	189	0.1585	3975	X-RAY DIFFRACTION	99
1.7671-1.8056	0.1807	207	0.16	3950	X-RAY DIFFRACTION	98
1.8056-1.8476	0.1732	208	0.167	3899	X-RAY DIFFRACTION	98
1.8476-1.8938	0.17	129	0.1679	2306	X-RAY DIFFRACTION	98
1.8938-1.945	0.1807	96	0.1675	1841	X-RAY DIFFRACTION	48
1.945-2.0022	0.184	148	0.1581	3195	X-RAY DIFFRACTION	79
2.0022-2.0668	0.1639	153	0.1579	3178	X-RAY DIFFRACTION	98
2.0668-2.1407	0.1669	173	0.1532	3360	X-RAY DIFFRACTION	97
2.1407-2.2264	0.154	212	0.1435	3913	X-RAY DIFFRACTION	98
2.2264-2.3277	0.1752	182	0.1348	3468	X-RAY DIFFRACTION	86
2.3277-2.4504	0.1413	222	0.1386	3944	X-RAY DIFFRACTION	99
2.4504-2.6039	0.1571	225	0.1425	4000	X-RAY DIFFRACTION	99
2.6039-2.8048	0.1751	199	0.1582	3670	X-RAY DIFFRACTION	91
2.8048-3.087	0.1661	197	0.1637	4022	X-RAY DIFFRACTION	99
3.087-3.5333	0.1693	200	0.1573	3790	X-RAY DIFFRACTION	94
3.5333-4.4503	0.1661	168	0.1398	3702	X-RAY DIFFRACTION	90
4.4503-36.2155	0.1857	228	0.1822	4032	X-RAY DIFFRACTION	97

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	5.3706	-1.9448	0.6389	5.3937	-1.0332	3.9693	-0.0926	-0.3306	-0.5196	0.2525	-0.0288	0.0188	0.3241	0.5507	0.0957	0.2101	0.0299	-0.0069	0.3249	0.0639	0.2221	14.813	5.5976	77.0629
2	2.7489	-0.5032	-1.708	0.6423	-0.2883	2.3003	0.0163	0.0152	0.1321	-0.1007	0.0448	0.1745	-0.3211	-0.3944	0.0003	0.2029	0.0197	-0.0295	0.295	0.0528	0.2709	3.1719	19.8441	66.8351
3	2.1751	0.6529	-1.2607	5.2297	-3.2934	4.3616	-0.1733	0.2408	-0.1356	-0.1345	0.1513	0.0916	0.2177	-0.1501	0.0009	0.1557	-0.0074	-0.0211	0.2235	0.0013	0.2178	3.0047	3.3426	68.7985
4	3.2904	0.7232	-0.3165	7.3928	-1.0611	3.3496	-0.1222	0.2137	-0.4945	-0.066	0.073	-0.1455	0.4398	0.0201	0.0468	0.1899	0.0007	0.0011	0.2537	-0.0163	0.2503	12.8807	2.2098	67.809
5	4.9518	-0.0851	-3.6935	2.2772	1.1654	6.9647	0.1745	0.0309	0.734	-0.161	0.1974	-0.0719	-0.7199	0.0468	-0.133	0.2543	-0.0299	-0.0144	0.2203	0.0229	0.3136	11.7377	23.4418	68.7192
6	5.2374	-3.0106	-0.9641	4.3255	0.6848	1.9533	-0.2026	-0.6071	0.2433	0.0904	0.2357	-0.0936	-0.0099	0.3409	-0.049	0.158	-0.0425	-0.0371	0.3301	0.0177	0.1979	21.9233	11.7434	74.2993
7	4.4884	-0.4422	1.2344	3.3624	-2.2022	6.2947	-0.0734	-0.1826	0.0065	0.2691	-0.0716	-0.2248	-0.2025	0.3214	0.1339	0.1758	0.0137	-0.0049	0.1968	0.0346	0.2428	0.4485	-2.2852	86.4835
8	4.51	-1.2066	-2.8016	1.3271	-0.6207	3.6658	0.1	0.6558	0.2347	-0.1703	-0.0347	0.0352	0.3004	-0.3408	-0.062	0.2232	0.0191	-0.0133	0.3643	0.1039	0.2568	-13.7945	2.8753	71.9699
9	7.5346	1.5219	0.1234	1.5149	0.2814	2.3196	0.2086	0.0574	0.4589	0.048	0.0259	0.2024	-0.1205	-0.0078	-0.1552	0.2111	0.0154	0.0221	0.1743	0.0518	0.2224	-2.5002	11.16	80.6927
10	5.2078	1.8014	0.4508	5.3884	0.5108	4.8096	0.205	-0.3994	0.2081	0.399	0.0027	-0.1806	-0.3176	0.2277	-0.1935	0.237	0.0056	0.0193	0.185	0.0009	0.2152	-4.808	5.7338	88.9903
11	4.7302	-1.1984	-3.305	3.0281	1.2208	6.3865	-0.0785	0.4507	-0.3529	-0.0949	0.018	0.4071	0.5109	-0.6398	0.0032	0.2292	-0.0478	-0.0434	0.2679	0.0528	0.2467	-16.0796	-5.3728	76.0669
12	1.3725	0.1775	-0.3622	1.6665	-1.2692	4.614	-0.0581	-0.0044	-0.0039	-0.1008	0.0088	0.0491	0.2069	0.1234	0.0562	0.1795	0.0095	-0.0046	0.1372	0.0243	0.2015	-6.6313	-8.4775	89.1526
13	7.0675	1.5455	2.4097	4.3471	1.0233	3.892	-0.0859	0.5729	-0.2257	-0.4595	0.0303	0.3619	0.3451	-0.5269	0.0273	0.2519	-0.0885	-0.0315	0.3278	-0.0243	0.1694	-33.226	6.7911	53.7296
14	2.7843	0.7201	-1.0372	1.6153	-1.0148	2.298	-0.1143	-0.2946	-0.2283	-0.143	-0.1138	-0.2898	0.2959	0.0684	0.1939	0.2011	0.0081	0.0187	0.219	0.0618	0.1977	-21.8542	3.3108	62.8065
15	2.8469	0.7053	-1.5862	1.5884	-0.3974	2.8198	-0.0483	-0.0914	-0.059	-0.0168	-0.0006	0.0933	0.2263	-0.2573	0.0385	0.1822	-0.0247	-0.0201	0.2169	0.0159	0.1692	-30.3041	9.1685	63.7675
16	8.3079	3.1316	-0.2882	2.3987	0.7111	1.407	0.0205	0.4475	0.3318	-0.0919	0.1151	0.2228	0.0208	-0.3978	-0.1203	0.1405	-0.008	-0.038	0.2749	0.0381	0.1697	-38.7637	13.839	58.1079
17	3.3626	-0.6045	0.341	5.9863	-3.2467	5.3189	0.0413	0.165	0.2519	-0.0461	0.0477	0.0999	-0.4281	-0.2275	-0.0496	0.2189	0.0182	0.019	0.1648	0.0036	0.2132	-13.9791	35.5277	51.9757
18	2.8623	-0.1582	-1.1062	2.7736	0.2102	1.4936	0.0228	-0.2012	-0.0963	0.029	0.0284	-0.1494	0.0295	0.1336	-0.0496	0.1633	-0.0164	-0.0243	0.1805	0.0162	0.1633	-5.3064	28.925	61.8845
19	3.4797	-0.234	-0.6372	7.2609	1.5566	4.0438	0.156	-0.1576	0.4495	-0.2471	-0.0686	-0.0692	-0.5525	0.1911	-0.0659	0.2607	-0.0497	0.0304	0.1804	0.0134	0.2665	-4.5068	37.088	53.1956
20	5.9786	0.2214	-3.7136	1.5585	-0.5437	3.6156	-0.4422	0.1542	-0.6841	-0.0861	0.1718	-0.1881	0.6437	0.0327	0.1919	0.307	-0.0189	0.0465	0.1864	-0.0269	0.3196	-8.1762	17.1246	50.5583
21	2.688	1.5809	-1.9735	5.884	-2.7921	3.2142	-0.0279	0.4242	0.1476	-0.2419	0.1792	0.0922	0.0911	-0.3487	-0.1311	0.2464	-0.0047	-0.0131	0.2112	0.0227	0.1826	-12.4909	31.1344	42.803
22	5.0216	-0.8117	1.1825	4.843	-0.9991	6.0869	-0.2336	0.4863	-0.1459	0.1045	-0.0082	0.4083	0.1276	-0.65	0.2246	0.286	-0.0661	0.0534	0.2763	-0.0741	0.2346	-21.7207	-2.3695	41.6797
23	7.1383	0.4384	-2.8158	1.0535	0.5198	3.3124	0.2191	-1.0277	-0.5111	1.0173	-0.0835	-0.2884	0.7665	0.5278	-0.0205	0.5871	0.0791	-0.0867	0.3919	0.0328	0.2711	-6.9097	-5.046	56.8851
24	5.675	-2.7453	-1.2394	4.0233	0.3519	2.5693	-0.0604	-0.081	0.2585	0.1317	0.2241	-0.2501	0.2234	0.0684	-0.1596	0.241	-0.0209	-0.0076	0.1742	-0.0481	0.1599	-15.4971	7.6458	50.9518
25	5.8792	-2.4576	0.6538	5.9781	-0.3387	4.3317	0.1016	0.2794	0.3399	-0.2482	-0.0951	0.028	-0.1729	-0.0819	-0.0398	0.2877	-0.017	0.0263	0.1871	-0.0199	0.2106	-14.6374	4.8974	41.3679
26	4.5286	0.5877	-3.1583	1.1246	0.6841	3.3638	-0.1923	-0.457	-0.8564	0.5546	0.1722	-0.3086	1.3253	0.6441	-0.0478	0.7333	0.1771	-0.0239	0.2948	0.0163	0.3867	-6.7166	-12.4629	50.6574
27	3.2414	-0.6579	0.4823	2.6572	-2.922	7.4826	-0.079	0.1246	-0.1955	0.2049	-0.039	0.0105	0.7172	-0.374	0.0097	0.3778	-0.0444	0.0608	0.1257	-0.0681	0.2459	-16.0867	-9.4353	37.4452

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 37 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 48 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 49 through 68 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 19 through 37 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 38 through 48 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 49 through 68 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 19 through 37 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 38 through 48 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 49 through 68 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 20 through 37 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 38 through 48 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 49 through 68 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 20 through 37 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 38 through 68 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 21 through 48 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 49 through 68 )
17	X-RAY DIFFRACTION	17	chain 'G' and (resid 20 through 37 )
18	X-RAY DIFFRACTION	18	chain 'G' and (resid 38 through 68 )
19	X-RAY DIFFRACTION	19	chain 'H' and (resid 20 through 37 )
20	X-RAY DIFFRACTION	20	chain 'H' and (resid 38 through 48 )
21	X-RAY DIFFRACTION	21	chain 'H' and (resid 49 through 68 )
22	X-RAY DIFFRACTION	22	chain 'I' and (resid 19 through 37 )
23	X-RAY DIFFRACTION	23	chain 'I' and (resid 38 through 48 )
24	X-RAY DIFFRACTION	24	chain 'I' and (resid 49 through 68 )
25	X-RAY DIFFRACTION	25	chain 'J' and (resid 19 through 37 )
26	X-RAY DIFFRACTION	26	chain 'J' and (resid 38 through 48 )
27	X-RAY DIFFRACTION	27	chain 'J' and (resid 49 through 68 )

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