PDB-5lbk: Crystal structure of the N-domain of HMA8, a copper-transporting ...

ID or keywords:

Entry

Database: PDB / ID: 5lbk

Title

Crystal structure of the N-domain of HMA8, a copper-transporting P-type ATPase

Components

Copper-transporting ATPase PAA2, chloroplastic

Keywords

HYDROLASE / P-type ATPase / copper transporter / chloroplast / thylakoid membrane / membrane protein

Function / homology

Function and homology information

P-type Cu2+ transporter / copper ion transmembrane transporter activity / P-type divalent copper transporter activity / copper ion transport / chloroplast thylakoid membrane / membrane => GO:0016020 / ATP binding / metal ion binding
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.75 Å

Authors

Mayerhofer, H. / Pebay-Peyroula, E. / Ravaud, S.

Funding support

France, 2items

Citation

Journal: PLoS ONE / Year: 2016
Title: Structural Insights into the Nucleotide-Binding Domains of the P1B-type ATPases HMA6 and HMA8 from Arabidopsis thaliana.
Authors: Mayerhofer, H. / Sautron, E. / Rolland, N. / Catty, P. / Seigneurin-Berny, D. / Pebay-Peyroula, E. / Ravaud, S.

History

Deposition	Jun 16, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 2, 2017	Provider: repository / Type: Initial release
Revision 1.1	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	5lbk.cif.gz	145.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5lbk.ent.gz	119.4 KB	Display	PDB format
PDBx/mmJSON format	5lbk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5lbk_validation.pdf.gz	434.6 KB	Display	wwPDB validaton report
Full document	5lbk_full_validation.pdf.gz	437.3 KB	Display
Data in XML	5lbk_validation.xml.gz	11.8 KB	Display
Data in CIF	5lbk_validation.cif.gz	16.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lb/5lbk ftp://data.pdbj.org/pub/pdb/validation_reports/lb/5lbk	HTTPS FTP

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Related structure data

Related structure data	5lbdC C: citing same article (ref.)
Similar structure data	3r5r-5 2pmc-1 2erm-d 3r5w-3 2gte-1 3cxg-2 3fe8-d 2p70-d 3r5w-8 1u8t-1 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
Related items in Molecule of the Month	#118 - Oct 2009 Sodium-Potassium Pump similarity (7) #51 - Mar 2004 Calcium Pump similarity (7)

Deposited unit

A: Copper-transporting ATPase PAA2, chloroplastic

B: Copper-transporting ATPase PAA2, chloroplastic

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

1

A: Copper-transporting ATPase PAA2, chloroplastic

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

2

B: Copper-transporting ATPase PAA2, chloroplastic

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

Unit cell

Length a, b, c (Å)	44.170, 48.280, 108.260
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Copper-transporting ATPase PAA2, chloroplastic / Protein HEAVY METAL ATPASE 8 Mass: 14513.306 Da / Num. of mol.: 2 / Fragment: UNP residues 557-689 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PAA2, HMA8, At5g21930, F13M11, T6G21 / Production host: Escherichia coli (E. coli) / References: UniProt: B9DFX7, Cu2+-exporting ATPase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Copper-transporting ATPase PAA2, chloroplastic / Protein HEAVY METAL ATPASE 8

Mass: 14513.306 Da / Num. of mol.: 2 / Fragment: UNP residues 557-689
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Gene: PAA2, HMA8, At5g21930, F13M11, T6G21 / Production host:

Escherichia coli (E. coli) / References: UniProt: B9DFX7, Cu2+-exporting ATPase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.99 Å³/Da / Density % sol: 38.14 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 0.1 M sodium acetate trihydrate pH 4.4, 0.6 M sodium formate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jun 14, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.953 Å / Relative weight: 1
Reflection	Resolution: 1.75→38.22 Å / Num. obs: 23737 / % possible obs: 99.4 % / Redundancy: 6 % / R_merge(I) obs: 0.065 / Net I/σ(I): 16.5
Reflection shell	Resolution: 1.75→1.86 Å / Redundancy: 6 % / R_merge(I) obs: 1.102 / Mean I/σ(I) obs: 2.64 / % possible all: 99

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Resolution: 1.75→36.031 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.72

	R_factor	Num. reflection	% reflection
R_free	0.2376	1160	4.95 %
R_work	0.1981	-	-
obs	0.2001	23419	97.21 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.75→36.031 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1774	0	0	125	1899

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	1810
X-RAY DIFFRACTION	f_angle_d	1.103	2446
X-RAY DIFFRACTION	f_dihedral_angle_d	14.606	1104
X-RAY DIFFRACTION	f_chiral_restr	0.071	294
X-RAY DIFFRACTION	f_plane_restr	0.008	311

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 (%)
1.75-1.8297	0.3471	150	0.2894	2790	X-RAY DIFFRACTION	99
1.8297-1.9261	0.2666	144	0.2542	2774	X-RAY DIFFRACTION	99
1.9261-2.0468	0.2307	157	0.2143	2777	X-RAY DIFFRACTION	99
2.0468-2.2048	0.2403	143	0.202	2783	X-RAY DIFFRACTION	98
2.2048-2.4267	0.2556	138	0.1979	2794	X-RAY DIFFRACTION	98
2.4267-2.7777	0.2289	143	0.2013	2772	X-RAY DIFFRACTION	97
2.7777-3.4991	0.2418	139	0.2058	2797	X-RAY DIFFRACTION	97
3.4991-36.0381	0.2209	146	0.1759	2772	X-RAY DIFFRACTION	91

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	9.6994	-0.1612	0.3263	6.7583	-1.1426	6.2925	-0.3718	-0.0774	1.0657	0.5175	0.215	-0.4187	-0.5474	0.409	0.0736	0.3721	-0.019	0.0347	0.3238	-0.0672	0.2634	31.9961	22.421	16.3685
2	6.2678	0.4556	-2.3053	2.6345	-0.7456	1.1946	0.0983	-0.7415	0.1713	-0.039	0.2065	-0.5318	-1.7307	0.8313	-0.179	0.5657	-0.1676	0.0555	0.421	-0.0731	0.3767	37.6512	25.5548	11.9223
3	8.9652	7.0705	-3.0043	7.0003	-2.9849	1.7689	-0.2791	2.3325	2.426	-0.7141	1.1655	0.8063	-2.3603	-0.1615	-0.4287	1.0384	0.048	0.0762	0.7074	0.1437	0.6442	30.6448	29.0723	0.0418
4	4.781	2.6563	-2.0231	3.6371	0.0212	1.5116	0.7329	0.4873	1.5866	-0.8571	-0.5857	1.0056	-1.4395	-0.5544	0.6323	1.1487	0.1523	0.1606	0.3361	0.0608	0.6053	29.0815	31.6921	8.1934
5	6.1464	-1.04	1.7852	2.1465	1.6707	2.4511	0.2874	0.2223	1.6789	0.6761	1.0899	-1.0077	-1.075	1.7319	-1.0701	1.2869	-0.3634	0.1671	0.541	-0.1419	0.6221	41.1788	31.3924	6.6864
6	2.6189	2.5253	-4.0814	2.3524	-4.0575	9.6667	-0.4635	0.3915	0.3728	-0.7335	0.6235	0.7564	0.0627	-1.1283	0.0228	0.264	-0.0381	0.0186	0.3718	0.0185	0.2821	31.665	19.0639	-4.5684
7	2.2595	-1.0687	2.3521	7.6566	-0.801	8.211	0.456	0.9037	0.7679	0.2742	-0.0634	-0.6305	-0.2367	1.3324	-0.3398	0.3078	-0.0631	0.0267	0.385	-0.0264	0.2137	41.8056	21.0889	1.8896
8	4.0524	0.9283	-2.46	7.9171	0.0229	5.8286	0.1601	0.4081	-0.4687	0.1398	-0.083	-0.1259	0.2165	0.3243	0.0776	0.1772	0.014	0.0325	0.2623	-0.0335	0.1724	35.1071	13.7127	2.9086
9	5.8007	1.7641	-6.9159	2.7448	-1.0989	8.9893	0.0717	-0.0956	-0.5203	0.4471	-0.2213	-0.3093	0.1883	1.5113	0.42	0.2885	0.0589	-0.0001	0.4558	-0.0015	0.4138	39.0314	6.7777	8.7412
10	9.7945	-4.6602	-1.8995	9.2664	0.7526	5.7611	0.0036	-0.175	-0.0696	-0.4544	0.435	-0.1185	0.0258	-0.3301	-0.3822	0.3874	-0.0468	0.0976	0.3328	0.0033	0.3554	29.3028	9.6827	18.3098
11	1.4814	-0.8095	0.3742	5.4224	1.1282	6.1703	0.376	-0.6654	-0.9555	0.4165	-0.3022	0.6221	-0.0094	-0.2819	-0.1176	0.2825	-0.0483	0.0425	0.3169	0.008	0.2184	27.5739	17.3339	11.9681
12	6.5025	-1.3734	-2.1175	7.6658	0.5943	6.7492	0.1101	0.1272	-0.1251	-0.3528	-0.2865	0.0409	-0.2052	0.1608	0.1253	0.2561	0.0093	-0.0123	0.1502	-0.022	0.0756	33.8494	17.2557	10.9443
13	5.1345	2.6395	-1.6015	3.1945	1.7459	5.0993	-0.0373	-0.503	-0.0707	0.0378	0.1249	-0.1539	0.751	1.1974	-0.355	0.3339	0.0362	-0.0327	0.2609	0.0144	0.2033	31.8501	24.9445	43.2596
14	6.7716	1.3625	0.9548	8.0019	0.5964	0.1751	-0.3067	-0.3745	-0.2746	0.1158	0.032	-0.6887	1.1899	0.9352	0.2606	0.3097	0.1583	0.0106	0.3755	0.0213	0.3359	35.1323	19.4534	36.4626
15	2.6581	1.3874	-0.0554	9.2569	4.282	2.1949	-0.5146	0.2014	0.0727	-1.0804	0.7355	-1.6011	-0.5768	1.1045	2.0996	0.0616	-0.0257	0.0358	0.8464	-0.0854	0.3799	40.941	26.5772	33.3617
16	3.158	2.6981	2.2533	3.2999	-0.0977	5.1588	0.2024	-1.273	-0.7986	0.528	-0.2385	-1.4171	1.6655	0.7976	-1.9436	0.5906	0.4513	-0.3103	0.8448	-0.0269	0.5269	39.7586	14.22	34.1049
17	0.3484	-1.5945	-1.0942	7.2669	4.9036	3.7483	0.4862	0.0651	0.388	-2.0974	0.0261	-0.5483	-1.021	0.3921	-0.0448	0.5439	0.0947	0.1261	0.2714	0.0392	0.2729	28.7246	25.5401	22.4196
18	2.7288	0.9057	-0.1321	4.8934	-4.3716	4.2611	-0.0479	0.0877	-0.5015	-0.0589	-0.1167	-0.2881	0.6167	0.1146	-0.1054	0.3473	0.0613	0.0639	0.1424	0.0181	0.3015	29.5994	15.1102	29.1432
19	5.6828	0.2685	-1.5054	5.861	0.3939	4.0888	-0.1352	0.1027	-0.1324	-0.0857	-0.1109	0.4539	0.6468	-0.4942	0.192	0.2766	-0.064	0.0118	0.2741	-0.0497	0.2089	20.6575	21.7289	31.7129
20	3.3457	2.461	2.6342	9.9081	3.3512	3.0969	0.1504	-0.0959	-0.0448	-0.151	-0.3019	0.6618	0.2598	0.0047	0.2303	0.3308	0.1048	0.0905	0.3379	-0.0105	0.3463	18.6622	28.3143	44.9122
21	6.1107	0.9148	0.9331	6.273	3.8434	6.1491	-0.1274	-0.0318	0.4612	0.1369	0.0064	0.2563	-0.3173	0.1144	-0.1088	0.313	-0.0198	0.0287	0.1747	-0.0083	0.1762	27.2556	29.2421	38.1407
22	5.0402	3.0302	1.6217	6.1745	2.5388	7.2516	-0.1001	0.1376	-0.0412	0.3439	0.0886	0.2163	0.1139	0.1326	0.0156	0.2072	0.002	0.0667	0.1817	-0.0076	0.1798	26.3294	23.5166	37.8128

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 558 through 569 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 570 through 580 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 581 through 586 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 587 through 598 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 599 through 608 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 609 through 615 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 616 through 623 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 624 through 637 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 638 through 643 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 644 through 654 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 655 through 676 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 677 through 688 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 558 through 569 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 570 through 583 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 584 through 598 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 599 through 608 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 609 through 615 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 616 through 623 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 624 through 643 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 644 through 653 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 654 through 676 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 677 through 688 )

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