PDB-5mg8: Crystal structure of the S.pombe Smc5/6 hinge domain

ID or keywords:

Entry

Database: PDB / ID: 5mg8

Title

Crystal structure of the S.pombe Smc5/6 hinge domain

Components

Structural maintenance of chromosomes protein 5
Structural maintenance of chromosomes protein 6

Keywords

RECOMBINATION / SMC / Structural Maintenance of Chromosomes /

Hinge Domain /

Smc5 /

Smc6 / Smc5/6

Function / homology

Function and homology information

SUMOylation of DNA damage response and repair proteins / division septum / Smc5-Smc6 complex / double-stranded DNA helicase activity / mitotic spindle pole body / sister chromatid cohesion / meiotic cell cycle / double-strand break repair via homologous recombination /

mitotic spindle /

single-stranded DNA binding ...
Similarity search - Function

Biological species

Schizosaccharomyces pombe (fission yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.75 Å

Authors

Alt, A. / Pearl, L.H. / Oliver, A.W.

Funding support

United Kingdom, 2items

Citation

Journal: Nat Commun / Year: 2017
Title: Specialized interfaces of Smc5/6 control hinge stability and DNA association.
Authors: Alt, A. / Dang, H.Q. / Wells, O.S. / Polo, L.M. / Smith, M.A. / McGregor, G.A. / Welte, T. / Lehmann, A.R. / Pearl, L.H. / Murray, J.M. / Oliver, A.W.

History

Deposition	Nov 21, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	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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Download

PDBx/mmCIF format	5mg8.cif.gz	452.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5mg8.ent.gz	371.6 KB	Display	PDB format
PDBx/mmJSON format	5mg8.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/mg/5mg8 ftp://data.pdbj.org/pub/pdb/validation_reports/mg/5mg8	HTTPS FTP

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Related structure data

Similar structure data	5odw-1 6nqu-d 2ysu-d 5odw-2 2dw4-d 4jlc-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) 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

Deposited unit

A: Structural maintenance of chromosomes protein 5

B: Structural maintenance of chromosomes protein 6

C: Structural maintenance of chromosomes protein 5

D: Structural maintenance of chromosomes protein 6

hetero molecules

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

1

A: Structural maintenance of chromosomes protein 5

B: Structural maintenance of chromosomes protein 6

hetero molecules

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

2

C: Structural maintenance of chromosomes protein 5

D: Structural maintenance of chromosomes protein 6

hetero molecules

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

Unit cell

Length a, b, c (Å)	172.564, 196.455, 122.440
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Structural maintenance of chromosomes protein 5 / DNA repair protein spr18 / SMC partner of rad18 Mass: 40301.633 Da / Num. of mol.: 2 / Fragment: UNP residues 366-692 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: smc5, spr18, SPAC14C4.02c / Production host: Escherichia coli (E. coli) / References: UniProt: O13710
#2: Protein	Structural maintenance of chromosomes protein 6 / DNA repair protein rad18 Mass: 33544.312 Da / Num. of mol.: 2 / Fragment: UNP residues 448-720 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: smc6, rad18, SPCC5E4.06 / Production host: Escherichia coli (E. coli) / References: UniProt: P53692
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.79 Å³/Da / Density % sol: 67.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM Bis-Tris pH7.5, 2.1M ammonium sulphate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 2, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.75→45.583 Å / Num. obs: 104437 / % possible obs: 100 % / Redundancy: 6.6 % / CC_1/2: 0.998 / R_merge(I) obs: 0.123 / R_pim(I) all: 0.056 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.75→2.86 Å / Redundancy: 6.7 % / R_merge(I) obs: 1.54 / Mean I/σ(I) obs: 1.4 / CC_1/2: 0.53 / R_pim(I) all: 0.979 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS	0.48 (24-Nov-2014)	data reduction
Aimless	0.5.14	data scaling
SHELXCD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.75→45.583 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 27.92

	R_factor	Num. reflection	% reflection
R_free	0.2494	5244	5.02 %
R_work	0.2087	-	-
obs	0.2108	104437	99.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.75→45.583 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8472	0	69	105	8646

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8737
X-RAY DIFFRACTION	f_angle_d	0.562	11839
X-RAY DIFFRACTION	f_dihedral_angle_d	7.605	6773
X-RAY DIFFRACTION	f_chiral_restr	0.037	1318
X-RAY DIFFRACTION	f_plane_restr	0.004	1538

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 (%)
2.75-2.7813	0.381	182	0.3554	3296	X-RAY DIFFRACTION	100
2.7813-2.814	0.38	190	0.3475	3205	X-RAY DIFFRACTION	100
2.814-2.8483	0.3243	171	0.3301	3408	X-RAY DIFFRACTION	100
2.8483-2.8844	0.3822	145	0.3317	3311	X-RAY DIFFRACTION	100
2.8844-2.9223	0.3321	165	0.3215	3293	X-RAY DIFFRACTION	100
2.9223-2.9623	0.335	199	0.3102	3279	X-RAY DIFFRACTION	100
2.9623-3.0046	0.3845	198	0.3197	3286	X-RAY DIFFRACTION	100
3.0046-3.0495	0.3577	195	0.3085	3334	X-RAY DIFFRACTION	100
3.0495-3.0971	0.3513	159	0.2918	3264	X-RAY DIFFRACTION	100
3.0971-3.1479	0.3075	180	0.2943	3349	X-RAY DIFFRACTION	100
3.1479-3.2022	0.3533	182	0.2976	3298	X-RAY DIFFRACTION	100
3.2022-3.2604	0.3269	169	0.2755	3340	X-RAY DIFFRACTION	100
3.2604-3.3231	0.3205	168	0.2639	3278	X-RAY DIFFRACTION	100
3.3231-3.3909	0.2771	164	0.2466	3328	X-RAY DIFFRACTION	100
3.3909-3.4646	0.3108	204	0.2425	3250	X-RAY DIFFRACTION	100
3.4646-3.5451	0.2784	162	0.2329	3304	X-RAY DIFFRACTION	100
3.5451-3.6338	0.237	184	0.2216	3341	X-RAY DIFFRACTION	100
3.6338-3.732	0.253	168	0.2033	3338	X-RAY DIFFRACTION	100
3.732-3.8417	0.246	176	0.1992	3289	X-RAY DIFFRACTION	100
3.8417-3.9657	0.2046	193	0.1856	3300	X-RAY DIFFRACTION	100
3.9657-4.1073	0.2381	165	0.1729	3289	X-RAY DIFFRACTION	100
4.1073-4.2716	0.218	198	0.1741	3279	X-RAY DIFFRACTION	100
4.2716-4.4659	0.1996	160	0.1675	3363	X-RAY DIFFRACTION	100
4.4659-4.7011	0.191	198	0.1542	3269	X-RAY DIFFRACTION	100
4.7011-4.9953	0.2	156	0.1512	3308	X-RAY DIFFRACTION	100
4.9953-5.3804	0.1648	141	0.167	3338	X-RAY DIFFRACTION	100
5.3804-5.9209	0.2815	135	0.188	3368	X-RAY DIFFRACTION	100
5.9209-6.7752	0.2335	164	0.1969	3304	X-RAY DIFFRACTION	100
6.7752-8.5269	0.2038	181	0.1715	3313	X-RAY DIFFRACTION	100
8.5269-45.5895	0.2101	192	0.1721	3271	X-RAY DIFFRACTION	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	7.9758	-4.5549	-2.1471	4.9267	4.0329	4.0003	-0.1364	0.3099	-1.6257	0.4538	-0.1502	1.0775	0.899	0.1113	-0.012	0.8706	-0.2088	0.1122	0.5616	-0.0634	0.7563	100.1949	6.9892	-22.6559
2	3.2806	0.7781	1.4343	2.7843	-1.1545	5.0411	-0.2509	0.3408	-0.0786	-0.5055	0.1608	-0.0706	0.1379	0.3488	0.093	0.6003	-0.1971	0.1019	0.4839	-0.0485	0.3918	111.6034	22.1098	-21.3073
3	4.6622	1.1439	2.9163	2.937	-0.191	5.477	0.1866	-0.1292	-0.2637	0.2443	-0.1278	-0.404	0.6237	0.2239	-0.1407	0.4737	-0.1006	0.032	0.3909	0.0202	0.3071	120.2931	17.0576	-1.7766
4	0.1004	-0.1813	0.0938	0.4496	-0.374	0.4791	0.0735	-0.1031	-0.4175	0.2417	0.1313	0.0651	0.0731	0.0808	-0.0197	0.5239	-0.1072	0.0866	0.5341	0.0865	0.7795	98.1682	0.999	-5.7678
5	2.9234	2.1239	-0.8336	1.7066	-1.1197	1.8464	-0.1903	-0.1226	-0.8569	0.1299	-0.3451	-0.7456	0.3838	0.0864	-1.3874	0.7421	-0.2307	-0.6088	0.6701	0.5076	2.1404	82.7386	-28.3655	-6.7156
6	6.1637	-0.4699	0.3084	1.9497	1.2581	6.0979	0.1081	-0.2113	-0.6043	0.9844	-0.3026	-0.5866	-0.695	-0.1497	0.1959	0.6456	-0.1296	0.0287	0.5568	0.0669	0.6628	91.5474	25.7173	-4.9083
7	1.8223	0.6869	0.3305	2.8026	-0.6465	2.8209	-0.0966	-0.1812	0.1002	0.2029	0.0728	0.2506	-0.2925	-0.069	0.0202	0.6237	-0.2086	0.0296	0.5093	-0.0106	0.4076	112.1657	42.359	-5.1759
8	4.3446	0.8133	0.4953	2.5651	1.7402	1.1814	-0.1994	0.0068	-1.3389	-0.1394	-0.3359	-0.692	1.4883	-0.411	0.5417	1.2723	0.1286	0.1298	0.5592	0.0075	0.818	67.8615	5.7643	23.5313
9	4.3212	-0.7276	0.296	3.2909	1.2063	3.1054	-0.3173	-0.8172	-0.4033	0.4476	0.1393	-0.188	0.53	-0.1972	0.0948	0.6707	0.312	0.0875	0.5985	0.0727	0.465	61.5345	17.2269	26.1083
10	4.8901	1.4857	2.6443	1.7088	1.4152	5.7337	-0.2927	-0.0487	-0.0576	0.151	0.2774	0.2334	-0.4734	0.2908	-0.0163	0.6201	0.2643	0.0366	0.4825	0.0502	0.385	55.0813	20.911	20.9099
11	5.1901	2.2506	0.7777	4.6283	1.4299	2.9769	-0.1342	-0.3487	0.0934	0.5136	0.1399	-0.2432	0.0354	-0.2675	0.1149	0.6186	0.3207	-0.0216	0.4959	0.0383	0.3445	53.7984	24.8202	26.6581
12	5.1368	1.3918	3.9499	5.629	2.0958	3.3267	0.1929	-0.1894	-0.7442	-0.0869	-0.1398	1.0399	1.0422	-1.107	0.1006	0.5885	0.0301	-0.0079	0.7269	0.0094	0.8042	38.4549	8.4136	8.3397
13	9.6841	0.769	5.9855	4.5843	1.5718	4.0082	0.0502	0.0529	-0.3458	-0.2535	0.0906	0.2386	0.2158	-0.1947	-0.1534	0.4713	0.075	0.0912	0.3277	0.0211	0.4119	45.1491	12.5112	8.6908
14	5.0408	-3.8188	1.0619	3.1094	-0.7799	2.0648	0.2945	0.5505	-0.7913	-0.7239	-0.2674	0.615	-0.4983	0.2451	-0.0003	0.7893	0.0929	-0.0209	0.6783	-0.0993	0.5707	38.7694	23.3951	0.4714
15	6.0687	1.4912	-1.2871	1.3484	-0.4648	0.5215	0.2616	1.0914	-0.9412	-0.6529	-0.6699	0.5029	0.8165	-0.4458	0.4163	1.0268	0.2445	-0.0165	0.8687	-0.2426	0.7553	63.2181	12.4173	8.4033
16	1.5306	-2.7747	0.0956	5.1576	-0.1036	0.9436	-0.4419	-0.409	-0.6759	0.6887	0.6949	0.7551	0.3529	-0.3065	-0.1694	0.3787	0.1207	0.0962	0.4995	0.0904	0.8701	87.492	-30.0248	14.0108
17	1.6002	-1.8425	0.8098	3.5881	-2.8187	2.7881	0.0186	-0.3545	-0.7855	-1.6093	0.5143	1.3432	0.6752	-0.4391	-0.3818	0.3503	-0.0315	-0.0574	0.4538	0.0306	0.8089	82.5233	-29.5592	8.7694
18	1.4605	0.1184	0.5812	0.0088	0.0447	0.231	0.3253	0.4373	-0.0396	-1.4194	-0.1473	-0.0135	0.4643	0.8439	-0.1832	1.5385	0.4381	0.2281	0.8829	0.1335	0.5257	72.3766	25.4322	2.3046
19	1.0728	1.2062	0.6222	1.8349	0.6553	1.7897	0.0461	0.6121	-0.2649	-0.6021	-0.0475	-0.2497	0.6444	0.421	0.0507	0.9429	0.3415	0.149	0.7888	-0.0219	0.5043	56.0316	37.8727	-4.9829
20	4.7121	0.5247	-2.0727	4.4487	1.3766	1.4994	-0.0262	0.9725	-1.1333	-0.6945	0.3773	-0.5244	1.0122	0.493	0.0194	1.141	0.3047	0.1516	0.9064	-0.1709	0.5803	51.1122	28.5392	-10.493
21	1.8629	0.722	1.5939	4.0762	1.2418	1.461	-0.09	0.316	0.0063	-0.5881	0.0548	-0.0982	0.07	0.1204	0.0787	0.8703	0.3219	0.0756	0.647	0.0228	0.4359	44.6738	39.0748	2.9453
22	5.733	-0.07	0.5687	3.7664	-1.566	3.323	-0.1044	-0.0001	0.1293	0.1546	0.1279	-0.1937	-0.1017	-0.0309	-0.0103	0.7606	0.3326	-0.0236	0.5642	-0.0573	0.3867	52.6729	36.8673	18.5055

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 408 through 432 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 433 through 532 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 533 through 584 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 585 through 689 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 449 through 494 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 495 through 521 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 522 through 712 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 411 through 432 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 433 through 469 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 470 through 502 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 503 through 523 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 524 through 544 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 545 through 584 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 585 through 623 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 624 through 635 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 636 through 690 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 448 through 498 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 499 through 523 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 524 through 571 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 572 through 597 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 598 through 644 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 645 through 711 )

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi