PDB-4u9q: Crystal structure of NqrA in spacegroup P21

ID or keywords:

Entry

Database: PDB / ID: 4u9q

Title

Crystal structure of NqrA in spacegroup P21

Components

Na(+)-translocating NADH-quinone reductase subunit A

Keywords

OXIDOREDUCTASE / sodium translocation / Rossmann fold

Function / homology

Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain / Na(+)-translocating NADH-quinone reductase subunit A (NQRA) / NQRA C-terminal domain / NADH:ubiquinone reductase (Na+-transporting) / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / Na(+)-translocating NADH-quinone reductase subunit A

Function and homology information

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.1 Å

Authors

Fritz, G.

Funding support

Germany, 1items

Citation

Journal: Nature / Year: 2014
Title: Structure of the V. cholerae Na+-pumping NADH:quinone oxidoreductase.
Authors: Steuber, J. / Vohl, G. / Casutt, M.S. / Vorburger, T. / Diederichs, K. / Fritz, G.

History

Deposition	Aug 6, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 3, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 17, 2014	Group: Database references
Revision 2.0	Dec 20, 2023	Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Refinement description Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_initial_refinement_model / pdbx_nonpoly_scheme Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4u9q.cif.gz	252.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4u9q.ent.gz	203.8 KB	Display	PDB format
PDBx/mmJSON format	4u9q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4u9q_validation.pdf.gz	432.7 KB	Display	wwPDB validaton report
Full document	4u9q_full_validation.pdf.gz	434.1 KB	Display
Data in XML	4u9q_validation.xml.gz	24.7 KB	Display
Data in CIF	4u9q_validation.cif.gz	35.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u9/4u9q ftp://data.pdbj.org/pub/pdb/validation_reports/u9/4u9q	HTTPS FTP

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Related structure data

Related structure data	4u9oSC 4u9sC 4u9uC 4uajC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5v01-d 3vxg-d 3c0l-d 3pic-1 4tuf-2 3tev-1 7k9a-2 2dym-1 3pic-2 6bh5-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: Na(+)-translocating NADH-quinone reductase subunit A

B: Na(+)-translocating NADH-quinone reductase subunit A

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

1

A: Na(+)-translocating NADH-quinone reductase subunit A

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

2

B: Na(+)-translocating NADH-quinone reductase subunit A

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

Unit cell

Length a, b, c (Å)	56.183, 81.703, 85.065
Angle α, β, γ (deg.)	90.00, 92.71, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NQR subunit A / NQR complex subunit A / NQR-1 subunit A Mass: 39121.918 Da / Num. of mol.: 2 / Fragment: UNP residues 1-357 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: nqrA, VC_2295 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9KPS1, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NQR subunit A / NQR complex subunit A / NQR-1 subunit A

Mass: 39121.918 Da / Num. of mol.: 2 / Fragment: UNP residues 1-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: nqrA, VC_2295 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9KPS1, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.49 Å³/Da / Density % sol: 50.65 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES NaOH pH 7.5, 25% PEG 3350, 0.2 M NaCl / PH range: 7.5-8.5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06SA / Wavelength: 1 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2012

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.1→45 Å / Num. obs: 44861 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / B_iso Wilson estimate: 31.26 Å² / R_merge F obs: 0.997 / R_merge(I) obs: 0.128 / R_rim(I) all: 0.147 / Χ²: 1.01 / Net I/σ(I): 8.02 / Num. measured all: 187588

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.1-2.2		0.558	1.351	1.2	24448	5815	5811	1.547	99.9
2.2-2.3		0.651	1.124	1.54	20418	4855	4851	1.286	99.9
2.3-2.5		0.803	0.814	2.28	31799	7529	7523	0.93	99.9
2.5-4		0.992	0.154	8.53	84558	20127	20100	0.175	99.9
4-5		0.997	0.052	22.43	12871	3186	3175	0.06	99.7
5-6		0.997	0.048	23.76	5728	1420	1418	0.055	99.9
6-10		0.998	0.041	25.76	6176	1550	1550	0.047	100
	10	0.998	0.034	27.15	1590	446	433	0.039	97.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
PHASER		phasing
PDB_EXTRACT	3.14	data extraction
Coot		model building
XSCALE		data scaling
XSCALE		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4U9O

4u9o

Resolution: 2.1→37.693 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 27.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.235	2241	5 %
R_work	0.2009	-	-
obs	0.2026	44817	99.7 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→37.693 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4625	0	0	287	4912

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4711
X-RAY DIFFRACTION	f_angle_d	0.756	6398
X-RAY DIFFRACTION	f_dihedral_angle_d	12.319	1737
X-RAY DIFFRACTION	f_chiral_restr	0.03	759
X-RAY DIFFRACTION	f_plane_restr	0.003	825

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 (%)
2.1-2.1457	0.3894	136	0.3687	2589	X-RAY DIFFRACTION	97
2.1457-2.1956	0.3833	139	0.3255	2642	X-RAY DIFFRACTION	100
2.1956-2.2505	0.3349	141	0.3062	2672	X-RAY DIFFRACTION	100
2.2505-2.3113	0.3315	139	0.2868	2640	X-RAY DIFFRACTION	100
2.3113-2.3793	0.3037	139	0.2708	2638	X-RAY DIFFRACTION	100
2.3793-2.4561	0.3399	140	0.2392	2670	X-RAY DIFFRACTION	100
2.4561-2.5439	0.3167	142	0.2513	2687	X-RAY DIFFRACTION	100
2.5439-2.6457	0.2526	138	0.2389	2615	X-RAY DIFFRACTION	100
2.6457-2.7661	0.2925	140	0.2282	2674	X-RAY DIFFRACTION	100
2.7661-2.9118	0.2446	141	0.2221	2664	X-RAY DIFFRACTION	100
2.9118-3.0942	0.2564	140	0.211	2660	X-RAY DIFFRACTION	100
3.0942-3.333	0.2041	140	0.2012	2663	X-RAY DIFFRACTION	100
3.333-3.6681	0.2201	141	0.1849	2675	X-RAY DIFFRACTION	100
3.6681-4.1983	0.1871	140	0.1546	2667	X-RAY DIFFRACTION	100
4.1983-5.2871	0.1614	141	0.1367	2675	X-RAY DIFFRACTION	99
5.2871-37.6995	0.1945	144	0.1582	2745	X-RAY DIFFRACTION	100

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	1.9986	0.4696	0.0271	3.7792	0.9813	1.1871	0.0186	0.0785	-0.1615	-0.0967	0.0214	-0.7085	-0.0103	0.1491	-0.0614	0.3124	-0.0082	0.0508	0.2999	0.0043	0.5211	-13.1312	10.3655	-41.6191
2	4.214	-0.6316	-0.1078	4.0957	0.1133	1.8576	-0.1343	0.2565	-0.3777	-0.2111	0.047	-0.2021	0.1652	-0.0587	0.0367	0.3599	-0.0737	0.0289	0.2234	-0.0332	0.4183	-23.052	6.8199	-43.7244
3	4.8634	0.9711	-0.9932	4.4306	1.0829	3.86	-0.1043	-0.2073	-0.0583	0.3864	-0.0796	0.5361	0.2491	-0.1559	0.0148	0.3217	0.0218	0.0125	0.2329	0.0655	0.3014	-29.7126	11.1969	-31.3685
4	5.8147	1.0818	-0.924	3.9814	0.115	1.5776	-0.0714	0.0867	0.9077	-0.1834	0.1485	-0.0024	-0.17	0.0674	-0.0962	0.272	0.0042	0.0442	0.1974	0.0151	0.4034	-25.1834	27.0492	-37.5522
5	3.3428	1.0925	0.8789	4.9363	-2.0486	3.7871	0.0993	-0.5166	0.4151	0.3899	-0.0697	0.5573	-0.3728	-0.3314	-0.05	0.3436	0.0087	0.1209	0.3047	-0.0596	0.4401	-32.8488	26.8427	-29.851
6	3.148	0.4791	-0.0845	2.7804	0.0905	0.853	0.0326	0.1665	-0.1717	-0.1992	0.0469	-0.6003	-0.1003	0.2482	-0.0966	0.3034	-0.0126	0.0369	0.2518	0.0058	0.3727	-15.9134	21.0999	-41.7173
7	6.0105	1.3391	-0.4794	3.6197	-0.2567	1.637	0.167	-0.4115	-0.0353	0.2308	0.0394	-0.9105	-0.0261	0.6341	-0.0879	0.3558	-0.0604	-0.076	0.4614	-0.0105	0.9312	-1.2111	19.2252	-32.8561
8	2.9061	0.286	-0.2501	3.9807	0.0368	2.694	0.1302	-0.343	-0.1985	0.0047	0.0117	-0.6952	0.0073	0.3958	-0.1061	0.3102	-0.01	-0.0432	0.3494	-0.0093	0.6244	-7.4796	16.4806	-33.7516
9	1.8633	-0.2479	0.1272	6.6633	0.7785	0.2665	0.0264	-0.015	-0.2644	0.296	-0.0228	-0.6895	0.0641	0.3272	-0.2106	0.3374	0.0184	-0.0271	0.4093	-0.0072	0.6804	-10.2944	32.378	-1.3465
10	2.6121	-0.1447	-0.3038	5.4351	1.7273	1.9726	-0.0006	0.1378	0.2264	-0.2364	0.1987	-0.5337	-0.3331	0.4292	-0.0263	0.2172	-0.0199	0.024	0.3155	-0.0247	0.4355	-19.1011	53.1506	-2.3134
11	5.063	1.3349	0.2494	3.9776	0.8247	3.4355	0.0325	-0.0551	0.507	-0.2363	0.0706	0.0195	-0.2096	0.0353	-0.0448	0.2954	0.0054	0.0032	0.214	-0.0297	0.4167	-20.5072	52.2834	-2.3092
12	6.0733	1.2444	-0.5215	3.2041	1.2959	3.1597	0.3666	-0.2773	-0.0715	0.4015	-0.182	-0.5328	-0.5664	0.2515	-0.0858	0.2917	0.08	-0.0058	0.1498	-0.0142	0.3297	-19.2681	48.41	1.9456
13	4.5712	1.1316	-1.0883	4.5885	-0.4685	3.5218	-0.0675	0.2095	0.2085	-0.1091	-0.0005	0.7041	-0.1262	-0.3841	0.086	0.2312	0.036	-0.0232	0.2677	-0.0037	0.4066	-35.5116	42.1602	-4.6219
14	4.517	0.3042	0.6412	5.1014	0.374	2.7284	-0.0444	0.1427	-0.0998	-0.0183	-0.038	0.2511	0.035	-0.0198	0.0888	0.1693	-0.0038	-0.0197	0.2341	-0.0128	0.2491	-31.2857	26.8983	-5.4781
15	0.9485	0.9596	-1.1338	3.1244	-0.1678	4.4698	-0.112	0.5593	-0.0191	-0.3553	-0.067	0.7687	-0.0769	-0.2923	0.0782	0.2509	0.0168	-0.1482	0.4396	0.0369	0.4481	-32.8441	27.0693	-17.6217
16	2.669	-0.0908	-0.8899	4.0791	0.7488	1.8723	-0.0269	-0.1012	0.0865	0.3415	0.0363	-0.2008	0.096	0.2091	-0.0684	0.1902	0.0125	-0.0131	0.2642	0.0182	0.2941	-25.1752	34.6377	-0.2685
17	4.0925	-1.5885	-1.7339	3.696	1.8102	3.2352	-0.017	0.2083	-0.0205	0.1664	0.0741	-0.7366	0.0659	0.186	-0.0385	0.2181	0.0343	-0.0099	0.409	-0.0163	0.737	-7.7527	31.6246	-3.6122
18	5.336	-1.8263	0.0554	2.7056	0.8584	2.0605	0.2929	0.6088	-0.2024	-0.6065	0.1185	-1.285	-0.2546	0.7521	-0.1519	0.3986	0.0155	0.1538	0.5585	-0.0614	0.8929	-4.2873	34.7972	-11.9389
19	2.2897	-0.3529	0.8657	2.7676	0.2226	1.626	-0.0437	0.4186	0.3587	-0.388	0.2298	-0.3268	0.0901	0.4048	-0.2055	0.3057	-0.0079	0.1319	0.4173	0.0369	0.6795	-10.0737	37.5979	-10.9826

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 14 through 56 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 57 through 126 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 127 through 148 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 149 through 185 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 186 through 236 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 237 through 287 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 288 through 311 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 312 through 329 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 15 through 33 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 34 through 56 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 57 through 81 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 82 through 107 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 108 through 148 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 149 through 206 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 207 through 236 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 237 through 266 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 267 through 287 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 288 through 311 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 312 through 330 )

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