PDB-6yso: Crystal structure of the (SR) Ca2+-ATPase solved by vanadium SAD ...

ID or keywords:

Entry

Database: PDB / ID: 6yso

Title

Crystal structure of the (SR) Ca2+-ATPase solved by vanadium SAD phasing

Components

Sarcoplasmic/endoplasmic reticulum calcium ATPase 1

Keywords

HYDROLASE /

P-type ATPase /

Vanadate / SAD phasing

Function / homology

Function and homology information

positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / H zone / positive regulation of fast-twitch skeletal muscle fiber contraction / calcium ion import into sarcoplasmic reticulum / regulation of striated muscle contraction / negative regulation of striated muscle contraction / positive regulation of ATPase-coupled calcium transmembrane transporter activity / P-type Ca2+ transporter / P-type calcium transporter activity ...
Similarity search - Function

Biological species

Oryctolagus cuniculus (rabbit)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.13 Å

Authors

El Omari, K. / Mohamad, N. / Bountra, K. / Duman, R. / Romano, M. / Schlegel, K. / Kwong, H. / Mykhaylyk, V. / Olesen, C.E. / Moller, J.V. ...

Citation

Journal: Iucrj / Year: 2020
Title: Experimental phasing with vanadium and application to nucleotide-binding membrane proteins.
Authors: El Omari, K. / Mohamad, N. / Bountra, K. / Duman, R. / Romano, M. / Schlegel, K. / Kwong, H.S. / Mykhaylyk, V. / Olesen, C. / Moller, J.V. / Bublitz, M. / Beis, K. / Wagner, A.

History

Deposition	Apr 22, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 4, 2020	Provider: repository / Type: Initial release
Revision 1.1	Dec 2, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6yso.cif.gz	782.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6yso.ent.gz	673.4 KB	Display	PDB format
PDBx/mmJSON format	6yso.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/ys/6yso ftp://data.pdbj.org/pub/pdb/validation_reports/ys/6yso	HTTPS FTP

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Related structure data

Related structure data	6yo1C C: citing same article (ref.)
Similar structure data	2o9j-d 4bew-2 3nal-d 4j2t-d 2c88-d 3n5k-1 4uu0-d 5a3s-1 3ar5-d 3fpb-d 3fgo-2 5zmv-d 3n5k-2 2by4-d 2c8k-d 3ar7-d 2yfy-d 3ar9-d 4ycm-d 4ycl-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

Related structure data

6yo1C

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	#118 - Oct 2009 Sodium-Potassium Pump similarity (19) #51 - Mar 2004 Calcium Pump similarity (19) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1

B: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1

hetero molecules

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

1

A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1

hetero molecules

defined by author
Evidence: gel filtration
111 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1

hetero molecules

defined by author
111 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	131.140, 94.390, 135.110
Angle α, β, γ (deg.)	90.00, 107.05, 90.00
Int Tables number	4
Space group name H-M	P12₁1
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 2 molecules AB

#1: Protein	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / SR Ca(2+)-ATPase 1 / Calcium pump 1 / Calcium-transporting ATPase sarcoplasmic reticulum type / ...SR Ca(2+)-ATPase 1 / Calcium pump 1 / Calcium-transporting ATPase sarcoplasmic reticulum type / fast twitch skeletal muscle isoform / Endoplasmic reticulum class 1/2 Ca(2+) ATPase Mass: 109602.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P04191, P-type Ca2+ transporter

#1: Protein

Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / SR Ca(2+)-ATPase 1 / Calcium pump 1 / Calcium-transporting ATPase sarcoplasmic reticulum type / ...

Mass: 109602.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural)

Oryctolagus cuniculus (rabbit) / References: UniProt: P04191, P-type Ca2+ transporter

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Non-polymers , 7 types, 22 molecules

#2: Chemical	ChemComp-128 / SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE Type: RNA linking / Mass: 718.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₁₆H₁₇N₈O₁₉P₃
#3: Chemical	ChemComp-TG1 / OCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OX Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER / THAPSIGARGIN / Thapsigargin Mass: 650.754 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₅₀O₁₂ / Comment: inhibitor*YM
#4: Chemical	ChemComp-VN4 / oxido(dioxo)vanadium Mass: 98.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 3.66 Å³/Da / Density % sol: 66.43 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 19% PEG2K MME, 11% Glycerol, 0.1M MgCl2, 6% 1-Butanol

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Data collection

Diffraction	Mean temperature: 60 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.26009 Å
Detector	Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 3, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 2.26009 Å / Relative weight: 1
Reflection	Resolution: 3.129→129.2 Å / Num. obs: 108998 / % possible obs: 99.9 % / Redundancy: 38.7 % / B_iso Wilson estimate: 98.3881401091 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.259 / R_pim(I) all: 0.059 / Net I/σ(I): 14.9
Reflection shell	Resolution: 3.129→3.22 Å / Redundancy: 34.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4573 / CC_1/2: 0.56 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
XSCALE		data scaling
CRANK2		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.13→64.585 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.6

	R_factor	Num. reflection	% reflection
R_free	0.2586	5498	5.04 %
R_work	0.201	-	-
obs	0.204	108998	99.8 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.13→64.585 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15168	0	200	8	15376

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	15675
X-RAY DIFFRACTION	f_angle_d	0.697	21237
X-RAY DIFFRACTION	f_dihedral_angle_d	16.504	9422
X-RAY DIFFRACTION	f_chiral_restr	0.043	2454
X-RAY DIFFRACTION	f_plane_restr	0.004	2697

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 (%)
3.13-3.1656	0.468	190	0.4068	3399	X-RAY DIFFRACTION	98
3.1656-3.2028	0.4114	195	0.3836	3402	X-RAY DIFFRACTION	99
3.2028-3.2419	0.3997	169	0.3578	3477	X-RAY DIFFRACTION	99
3.2419-3.2829	0.393	156	0.3408	3462	X-RAY DIFFRACTION	100
3.2829-3.3261	0.3368	187	0.3018	3377	X-RAY DIFFRACTION	100
3.3261-3.3716	0.3465	177	0.2966	3575	X-RAY DIFFRACTION	100
3.3716-3.4198	0.3506	176	0.2862	3420	X-RAY DIFFRACTION	100
3.4198-3.4709	0.3928	168	0.2918	3454	X-RAY DIFFRACTION	100
3.4709-3.5251	0.3164	181	0.2681	3473	X-RAY DIFFRACTION	100
3.5251-3.5829	0.2925	183	0.252	3433	X-RAY DIFFRACTION	100
3.5829-3.6447	0.3002	179	0.2406	3483	X-RAY DIFFRACTION	100
3.6447-3.7109	0.3059	188	0.2457	3392	X-RAY DIFFRACTION	100
3.7109-3.7823	0.2871	213	0.2361	3465	X-RAY DIFFRACTION	100
3.7823-3.8595	0.3101	174	0.2181	3508	X-RAY DIFFRACTION	100
3.8595-3.9434	0.2599	186	0.2089	3419	X-RAY DIFFRACTION	100
3.9434-4.0351	0.2291	180	0.1858	3451	X-RAY DIFFRACTION	100
4.0351-4.136	0.2284	185	0.1653	3429	X-RAY DIFFRACTION	100
4.136-4.2478	0.2033	206	0.162	3447	X-RAY DIFFRACTION	100
4.2478-4.3728	0.211	204	0.1686	3435	X-RAY DIFFRACTION	100
4.3728-4.5139	0.2114	189	0.1635	3474	X-RAY DIFFRACTION	100
4.5139-4.6752	0.2161	203	0.1548	3431	X-RAY DIFFRACTION	100
4.6752-4.8623	0.219	183	0.162	3443	X-RAY DIFFRACTION	100
4.8623-5.0835	0.2174	188	0.1607	3446	X-RAY DIFFRACTION	100
5.0835-5.3514	0.2287	155	0.1784	3468	X-RAY DIFFRACTION	100
5.3514-5.6865	0.2663	162	0.1896	3512	X-RAY DIFFRACTION	100
5.6865-6.1252	0.2534	172	0.2022	3470	X-RAY DIFFRACTION	100
6.1252-6.7411	0.2557	185	0.2077	3446	X-RAY DIFFRACTION	100
6.7411-7.7151	0.2466	192	0.1842	3463	X-RAY DIFFRACTION	100
7.7151-9.7149	0.2366	186	0.1545	3435	X-RAY DIFFRACTION	100
9.7149-64.585	0.2537	186	0.1918	3411	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	3.3764	-2.168	0.9289	1.6727	-0.7506	1.8568	0.1189	0.1587	-0.1296	-0.2897	-0.1426	0.3553	0.3547	-1.1899	-0.0638	0.8568	-0.0722	-0.2979	1.59	-0.0601	1.1802	70.5727	28.0883	1.433
2	0.9705	-0.4126	1.5224	0.8165	0.3795	2.4716	-0.2821	0.0491	-0.0662	-0.2731	-0.0047	0.722	-0.5727	-0.6469	0.0478	1.0593	0.1142	-0.3539	1.1074	0.0518	1.3288	73.5436	39.7642	-8.0981
3	1.4778	-1.1139	-0.5346	1.9262	-0.4068	0.8409	0.0539	0.9422	0.1969	-0.4396	-0.2744	0.7029	-0.175	-0.6573	0.1759	1.1221	0.1007	-0.423	1.5182	-0.0135	1.1246	75.3063	36.9511	-23.8033
4	2.4573	0.1992	-1.0092	2.2249	0.6173	3.9024	-0.1705	-0.3094	-0.0296	0.5281	0.1554	0.1961	0.3793	-0.2082	0.0032	0.7113	0.0082	0.0421	0.603	-0.0251	0.5151	108.41	17.4831	34.8753
5	4.6405	1.8173	6.673	0.7315	2.6573	9.6551	-0.5385	1.712	0.3619	-0.6387	-0.3372	1.2772	0.1693	-1.8668	0.7291	1.0605	-0.1211	-0.0636	1.7802	-0.3458	1.321	84.12	22.7729	18.1846
6	2.1803	-2.3649	2.2397	4.7798	-4.6904	4.621	0.1194	-0.7715	0.9442	-0.2543	1.1894	0.7962	-1.5472	0.0374	-0.6215	1.9655	0.3798	0.2594	0.9273	0.187	1.1918	93.9549	31.8709	11.384
7	3.4291	0.0106	1.9958	3.7093	0.7259	4.308	-0.1491	0.0355	0.3258	-0.4737	0.032	0.098	-0.4083	-0.0558	0.1362	0.5878	-0.0079	0.0581	0.4465	0.0014	0.5783	110.6375	29.2037	5.7515
8	4.0515	0.7328	-0.0795	2.4911	0.0964	1.925	0.0103	-0.0172	-0.0894	0.1968	0.0175	-0.2341	0.0763	0.3048	-0.0434	0.7798	0.0735	0.0182	0.5335	-0.0256	0.7021	134.4983	3.9261	13.3681
9	7.2009	3.2741	2.6502	2.6628	1.9252	1.9638	-0.3313	-0.7806	0.3671	-0.1742	0.0577	0.936	-0.179	-0.7374	0.3661	0.9326	-0.0406	-0.2162	0.8904	0.2572	1.1535	63.6716	59.1959	21.5438
10	3.7035	1.171	2.9325	0.1429	0.5042	3.1433	-0.1497	0.3485	-0.8141	-0.0459	0.2154	-0.3697	-0.1792	0.6606	0.0114	0.9713	-0.0125	0.0145	1.0427	0.1065	1.3545	59.0285	44.973	23.1316
11	1.8257	0.6036	1.1509	-0.7897	0.9222	0.0999	0.5097	-1.0796	-1.5221	0.0529	-0.3187	0.0037	0.4475	-0.4851	-0.2374	1.1233	-0.2848	-0.3065	1.6361	0.6113	2.1819	52.1679	40.7703	37.2412
12	1.8153	0.765	0.2474	3.7812	-1.7329	4.113	-0.0464	0.1812	-0.1119	-0.4242	0.1735	0.0855	-0.0074	0.0409	-0.1265	0.7191	0.0327	0.0645	0.5337	-0.0061	0.5971	114.3287	71.3546	23.5153
13	5.6997	-0.582	4.1648	0.0542	-0.425	3.0461	-0.1176	0.3251	-0.7915	-0.0813	-0.3573	0.959	-0.1633	-0.0702	0.2969	1.5738	-0.1465	-0.3065	1.3073	0.423	1.9359	85.9389	65.513	16.8967
14	9.8693	6.9221	-1.8598	6.0728	-1.1698	1.4183	-0.5851	0.035	-0.5714	-0.3224	-0.2354	1.1115	-0.159	0.5305	0.6828	1.5358	-0.2324	-0.24	1.1871	0.2474	1.5128	88.4629	54.3269	25.8207
15	5.0826	0.0392	-0.0844	2.076	-0.6553	2.9519	0.1066	-0.2938	-0.9031	0.2524	0.0527	0.083	0.3383	-0.2703	-0.1781	0.875	-0.0642	-0.1091	0.6814	0.1395	0.9045	98.3551	50.0138	39.9288
16	3.7349	0.1446	0.399	2.256	-0.0239	3.034	-0.1168	-0.1915	0.172	0.0194	0.0951	0.1194	-0.251	0.2548	0.0734	0.9033	0.0572	0.054	0.8199	0.059	0.62	122.0217	68.8347	59.0238

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and (resid 50:122)
2	X-RAY DIFFRACTION	2	chain A and (resid 248:329)
3	X-RAY DIFFRACTION	3	chain A and (resid 741:994)
4	X-RAY DIFFRACTION	4	chain A and (resid 1:41 or resid 123:237)
5	X-RAY DIFFRACTION	5	chain A and (resid 42:49)
6	X-RAY DIFFRACTION	6	chain A and (resid 238:247)
7	X-RAY DIFFRACTION	7	chain A and (resid 330:358 or resid 604:740)
8	X-RAY DIFFRACTION	8	chain A and (resid 359:603)
9	X-RAY DIFFRACTION	9	chain B and (resid 50:122)
10	X-RAY DIFFRACTION	10	chain B and (resid 248:329)
11	X-RAY DIFFRACTION	11	chain B and (resid 741:994)
12	X-RAY DIFFRACTION	12	chain B and (resid 1:41 or resid 123:237)
13	X-RAY DIFFRACTION	13	chain B and (resid 42:49)
14	X-RAY DIFFRACTION	14	chain B and (resid 238:247)
15	X-RAY DIFFRACTION	15	chain B and (resid 330:358 or resid 604:740)
16	X-RAY DIFFRACTION	16	chain B and (resid 359:603)

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