PDB-7dqc: Crystal structure of nucleotide-free mutant A(S23C)3B(N64C)3 comp...

ID or keywords:

Entry

Database: PDB / ID: 7dqc

Title

Crystal structure of nucleotide-free mutant A(S23C)3B(N64C)3 complex from Enterococcus hirae V-ATPase

Components

V-type sodium ATPase catalytic subunit A
V-type sodium ATPase subunit B

Keywords

HYDROLASE / V-ATPase / A3B3 / asymmetric structure

Function / homology

Function and homology information

Na+-transporting two-sector ATPase / sodium-transporting ATPase activity, rotational mechanism / proton motive force-driven plasma membrane ATP synthesis / sodium ion transport / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ATP binding
Similarity search - Function

Biological species

Enterococcus hirae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.706 Å

Authors

Maruyama, S. / Suzuki, K. / Mizutani, K. / Imai, F.L. / Ishizuka-Katsura, Y. / Shirouzu, M. / Murata, M.

Citation

Journal: To Be Published
Title: The combination of high-speed AFM and X-ray crystallography reveals rotary catalytic mechanism of shaftless V1-ATPase
Authors: Imamura, M. / Maruyama, S. / Nakamoto, K. / Kawai, F. / Akiyama, T. / Mizutani, K. / Suzuki, K. / Shirouzu, M. / Iino, R. / Uchihashi, T. / Ando, T. / Murata, T.

History

Deposition	Dec 23, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 29, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	7dqc_validation.pdf.gz	528.5 KB	Display	wwPDB validaton report
Full document	7dqc_full_validation.pdf.gz	664.3 KB	Display
Data in XML	7dqc_validation.xml.gz	119.3 KB	Display
Data in CIF	7dqc_validation.cif.gz	160.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dq/7dqc ftp://data.pdbj.org/pub/pdb/validation_reports/dq/7dqc	HTTPS FTP

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Related structure data

Related structure data	3vr2S S: Starting model for refinement
Similar structure data	5zea-1 7cor-d 3vr2-d 7cop-d 7coq-d 7cos-2 7cos-1 5zea-2 7dqe-d 3vr3-d 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	#219 - Mar 2018 Vacuolar ATPase similarity (13) #131 - Nov 2010 Inteins similarity (12) #72 - Dec 2005 ATP Synthase similarity (9)

Deposited unit

A: V-type sodium ATPase catalytic subunit A

B: V-type sodium ATPase catalytic subunit A

D: V-type sodium ATPase subunit B

E: V-type sodium ATPase subunit B

C: V-type sodium ATPase catalytic subunit A

F: V-type sodium ATPase subunit B

hetero molecules

355 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	122.080, 121.830, 129.110
Angle α, β, γ (deg.)	90.000, 90.220, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	V-type sodium ATPase catalytic subunit A / Na(+)-translocating ATPase subunit A / V-type sodium pump catalytic subunit A Mass: 66363.867 Da / Num. of mol.: 3 / Mutation: S23C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258) (bacteria) Gene: ntpA, EHR_08260 / Production host: Escherichia coli (E. coli) References: UniProt: Q08636, Na+-transporting two-sector ATPase
#2: Protein	V-type sodium ATPase subunit B / Na(+)-translocating ATPase subunit B / V-type sodium pump subunit B Mass: 51709.938 Da / Num. of mol.: 3 / Mutation: N64C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258) (bacteria) Gene: ntpB, EHR_08265 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08637
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.71 Å³/Da / Density % sol: 54.62 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion / pH: 8.5 / Details: 25% PEG 3350, 100mM MES-Tris pH 8.5, 100mM NaCl

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-17A / Wavelength: 0.98 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 21, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 2.706→44.304 Å / Num. obs: 102939 / % possible obs: 99.8 % / Redundancy: 4.02 % / B_iso Wilson estimate: 61.64 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.077 / R_rim(I) all: 0.089 / Χ²: 1.109 / Net I/σ(I): 15.06

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.71-2.87	4.07	0.666	2.03	67081	16603	16482	0.692	0.765	99.3
2.87-3.07	3.919	0.422	3.19	60933	15568	15549	0.831	0.489	99.9
3.07-3.31	4.169	0.252	5.57	60563	14533	14528	0.946	0.289	100
3.31-3.63	3.97	0.134	10.02	52840	13324	13311	0.983	0.155	99.9
3.63-4.05	4.055	0.076	17.29	49159	12134	12123	0.994	0.088	99.9
4.05-4.67	4.022	0.044	28.58	43125	10738	10723	0.998	0.051	99.9
4.67-5.7	4.041	0.04	30.65	36629	9075	9064	0.998	0.045	99.9
5.7-8	3.911	0.035	33.83	27748	7109	7095	0.999	0.04	99.8
8-44.304	3.875	0.02	54.02	15747	4105	4064	0.999	0.023	99

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R rigid body: 0.509

	Highest resolution	Lowest resolution
Rotation	44.31 Å	2.98 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
MOLREP		phasing
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3VR2

3vr2

Resolution: 2.706→44.304 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2661	5266	5.12 %
R_work	0.2342	97651	-
obs	0.2358	102917	99.76 %

Solvent computation

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

Displacement parameters

B_iso max: 215.21 Å² / B_iso mean: 83.6003 Å² / B_iso min: 22.72 Å²

Refinement step

Cycle: final / Resolution: 2.706→44.304 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23490	0	84	286	23860
B_iso mean	-	-	110.49	61.61	-
Num. residues	-	-	-	-	3104

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	23930
X-RAY DIFFRACTION	f_angle_d	0.576	32421
X-RAY DIFFRACTION	f_chiral_restr	0.025	3666
X-RAY DIFFRACTION	f_plane_restr	0.002	4273
X-RAY DIFFRACTION	f_dihedral_angle_d	13.228	8808

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.706-2.7368	0.3745	194	0.3146	3138	97
2.7368-2.769	0.3313	151	0.3141	3301	100
2.769-2.8027	0.3466	179	0.3011	3169	100
2.8027-2.8382	0.2835	199	0.2919	3256	100
2.8382-2.8755	0.3215	195	0.2883	3241	100
2.8755-2.9149	0.3261	177	0.2908	3235	100
2.9149-2.9566	0.33	188	0.2854	3203	100
2.9566-3.0007	0.3175	189	0.2822	3231	100
3.0007-3.0476	0.3469	221	0.2876	3203	100
3.0476-3.0975	0.3513	176	0.291	3224	100
3.0975-3.1509	0.3377	184	0.2704	3243	100
3.1509-3.2082	0.3135	200	0.2647	3281	100
3.2082-3.2699	0.2771	164	0.2531	3217	100
3.2699-3.3366	0.2737	188	0.2548	3221	100
3.3366-3.4091	0.2927	157	0.2556	3325	100
3.4091-3.4884	0.2511	147	0.2392	3283	100
3.4884-3.5756	0.2864	156	0.233	3249	100
3.5756-3.6722	0.2669	144	0.2341	3272	100
3.6722-3.7802	0.2392	194	0.228	3253	100
3.7802-3.9022	0.2572	149	0.2328	3250	100
3.9022-4.0415	0.278	195	0.2295	3255	100
4.0415-4.2032	0.2753	158	0.2172	3302	100
4.2032-4.3944	0.2321	166	0.2103	3236	100
4.3944-4.6258	0.2569	145	0.1947	3301	100
4.6258-4.9153	0.2247	139	0.2093	3320	100
4.9153-5.2942	0.2454	158	0.2354	3283	100
5.2942-5.826	0.2455	224	0.2525	3232	100
5.826-6.6665	0.2679	202	0.2458	3247	100
6.6665-8.3898	0.2337	175	0.2123	3307	100
8.3898-44.304	0.2074	152	0.1845	3373	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	3.7725	-0.417	-1.971	5.1096	-2.2327	7.9474	-0.2447	-0.2873	-0.0869	0.2297	0.2845	-0.146	-0.2282	0.0847	-0.027	0.4009	0.0794	-0.0047	0.3247	-0.029	0.4083	53.5241	6.8025	197.4496
2	2.6579	-0.3399	-0.0037	0.8367	-0.1745	1.7175	-0.0785	-0.5161	-0.031	0.2269	0.0695	0.1408	-0.0681	0.0143	0.0085	0.3758	0.002	0.0035	0.3458	0.0101	0.3904	66.1191	-11.3374	198.852
3	1.9534	-0.1603	0.1863	1.38	-0.1914	1.9971	-0.0129	0.0426	0.0963	0.0156	0.0028	-0.0287	0.029	0.002	0.0056	0.343	-0.0001	0.0388	0.2183	-0.0048	0.3109	70.6336	-12.8436	182.6363
4	2.1482	-1.5576	0.1316	3.9832	1.1432	3.2782	0.3768	0.6937	-0.5562	-0.9091	-0.3009	0.384	0.8304	-0.0958	-0.0676	1.0039	0.0174	-0.0711	0.5452	-0.0916	0.4482	66.1252	-35.291	157.9634
5	1.8314	0.1089	0.2929	0.902	-1.3079	7.5279	-0.0696	0.2343	0.4493	-0.2768	0.0306	-0.1802	-0.3823	-0.2171	0.0304	0.4469	-0.0384	0.0231	0.3767	0.0933	0.5712	44.9253	35.5024	162.2686
6	3.1277	0.1155	-0.6108	0.9799	-0.2062	1.254	-0.0648	0.4333	0.809	-0.468	0.1368	0.0499	-0.4102	-0.2368	-0.0855	0.9595	-0.0206	0.0141	0.6362	0.2029	0.739	39.3754	47.5396	140.5044
7	2.3671	-0.4172	0.16	2.5683	0.7084	0.857	-0.0145	0.2835	0.1052	-0.4568	0.1307	0.0606	0.0085	-0.3319	-0.1325	0.6396	-0.1151	-0.0102	0.7695	0.1472	0.4219	33.8342	26.5496	141.3573
8	4.5907	-0.3194	-1.3079	4.5953	4.588	9.2678	-0.0563	-0.1154	-0.8718	-0.1135	0.4068	0.247	1.3463	-0.4631	-0.2825	0.8971	-0.1783	-0.0207	0.8074	0.1627	0.5845	29.361	10.6529	144.1562
9	3.3922	0.7353	0.9003	1.9842	1.8429	4.0516	0.2849	0.3043	-0.7296	-0.6551	-0.0903	0.8731	0.4437	-0.7031	0.0849	1.034	-0.2763	-0.1942	0.8959	0.1134	0.6704	21.3235	7.4704	126.6406
10	3.4738	0.7247	1.1115	1.8537	1.7891	4.2401	-0.3953	1.2277	-0.3469	-1.2289	0.3517	0.433	-0.0492	-0.2737	-0.0374	1.4377	-0.2372	-0.1913	1.3299	0.0072	0.794	23.3671	4.6908	111.313
11	1.7209	-1.3295	0.4467	2.2145	-0.9109	1.9941	-0.3395	-0.4998	-0.2508	0.7171	0.6496	1.1957	-0.2944	-0.7248	-0.2465	0.5239	0.1826	0.194	0.7794	0.2621	0.8464	30.2384	4.008	205.3486
12	3.3569	-0.8333	0.3438	3.922	-0.2007	4.0116	0.1493	-0.0194	0.1487	-0.2542	0.4068	0.9451	-0.0242	-0.6634	-0.5049	0.3884	0.0227	0.0514	0.5351	0.2809	0.8521	33.6817	-21.2219	192.9938
13	4.8902	0.9395	-0.5118	4.3322	1.8423	7.1187	-0.0563	1.1821	-0.9508	-1.7256	0.3537	0.4793	1.1623	-0.4767	-0.2906	1.3986	-0.1493	-0.2132	0.834	-0.0451	1.006	34.2007	-41.7248	173.7808
14	1.2117	-0.2421	-0.6232	1.3834	0.4614	3.3038	-0.2157	0.0694	0.1007	-0.2383	0.2142	-0.447	-0.042	0.3056	0.0667	0.394	-0.0887	0.0511	0.3778	-0.0028	0.5201	63.698	20.2639	177.3166
15	2.7476	-0.394	1.4902	5.2152	-1.4564	2.7013	-0.0132	0.4993	0.211	0.09	-0.0161	-0.5202	-0.516	0.4106	-0.1344	0.5474	-0.0122	0.1582	0.6085	0.0747	0.6078	68.9849	17.0035	154.1944
16	5.2648	-1.9247	3.081	5.7306	0.4673	8.6534	0.5511	0.8797	0.0453	-1.4365	-0.2838	-0.4723	0.9809	0.6333	-0.2614	0.8843	0.2771	0.0664	0.6034	0.0286	0.4688	64.8147	1.4877	143.5223
17	2.9484	-0.0985	-2.0119	4.8975	-1.6613	8.3407	0.2072	0.1754	0.2371	-0.3753	-0.1685	-0.5157	0.0642	0.5631	-0.0132	0.3855	0.0108	0.0507	0.3466	0.0346	0.4079	66.8361	6.2171	156.9378
18	3.4762	-1.141	2.4252	4.9504	1.9288	5.1675	0.2124	-0.0086	0.2914	-0.1532	-0.1769	0.5112	-0.1872	-0.6484	-0.0402	0.6254	0.1167	0.0059	0.4231	-0.0097	0.4376	54.162	11.6612	154.249
19	7.6401	-1.8021	-1.542	6.3456	0.2516	6.7904	0.7694	0.0522	-0.4251	-0.9409	-0.0314	0.8586	1.3105	-0.803	-0.7558	1.0683	0.0515	-0.2824	0.6926	0.0908	0.6492	53.1287	-2.5511	144.2765
20	2.6195	-0.894	1.0476	0.622	0.7021	3.7743	0.7874	0.3234	-1.2682	-1.8217	-0.3705	0.8344	2.1621	0.264	-0.4353	2.8311	0.3703	-0.6571	0.7857	-0.0863	1.139	56.3233	-13.3776	129.4038
21	0.6275	0.4201	-0.0728	1.5562	-0.1203	0.2598	0.0575	-0.0202	0.0402	0.0327	0.0704	0.363	-0.0509	-0.3176	-0.1323	0.448	0.0952	0.0186	0.7678	0.2101	0.8002	-0.1973	2.4449	192.6929
22	0.8522	0.4094	0.4116	3.3427	1.1946	1.0678	0.1394	0.5489	-0.0098	-0.8941	-0.0861	-0.3506	-0.0737	-0.0798	-0.0157	0.7572	0.2035	0.0469	1.0378	0.1792	0.7771	3.409	-21.556	174.4835
23	3.5601	1.9522	1.8669	1.3942	0.8277	1.5437	-0.2844	0.3449	0.9045	-0.4488	0.0917	0.5297	-0.5301	-0.5437	0.062	0.545	0.1363	-0.0269	0.6985	0.1683	0.7594	16.9882	35.0465	169.8186
24	4.4356	0.8941	-0.8587	3.0621	-0.2891	3.9841	-0.4389	0.9785	-0.4961	-0.6879	0.2388	0.7469	0.5231	-1.1873	0.1799	0.6831	-0.1497	-0.1366	0.9899	0.1589	0.8863	-1.7166	12.9992	156.233
25	8.1436	0.8087	-1.8065	3.4666	0.327	5.2096	-0.0867	0.5578	0.0246	-0.3337	0.2639	0.2702	-0.0017	-0.2403	-0.1789	0.4825	-0.0563	-0.1015	0.6272	0.1747	0.5775	8.2015	19.0271	159.7745
26	1.6289	0.2074	-0.5114	3.4608	0.8839	2.7029	-0.4491	0.8287	-1.0102	-0.5931	0.2198	0.4497	0.949	-0.2723	0.2162	1.0704	-0.207	-0.0433	1.1377	-0.1195	1.31	0.381	-3.4497	145.8099

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 62 )	A	1 - 62
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 63 through 120 )	A	63 - 120
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 121 through 380 )	A	121 - 380
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 381 through 586 )	A	381 - 586
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 90 )	B	1 - 90
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 91 through 178 )	B	91 - 178
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 179 through 389 )	B	179 - 389
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 390 through 416 )	B	390 - 416
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 417 through 477 )	B	417 - 477
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 478 through 586 )	B	478 - 586
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 5 through 85 )	D	5 - 85
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 86 through 330 )	D	86 - 330
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 331 through 452 )	D	331 - 452
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 2 through 85 )	E	2 - 85
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 86 through 125 )	E	86 - 125
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 126 through 187 )	E	126 - 187
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 188 through 263 )	E	188 - 263
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 264 through 305 )	E	264 - 305
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 306 through 362 )	E	306 - 362
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 363 through 451 )	E	363 - 451
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 1 through 284 )	C	1 - 284
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 285 through 584 )	C	285 - 584
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 4 through 106 )	F	4 - 106
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 107 through 186 )	F	107 - 186
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 187 through 296 )	F	187 - 296
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 297 through 453 )	F	297 - 453

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