PDB-4oh3: Crystal structure of a nitrate transporter

ID or keywords:

Entry

Database: PDB / ID: 4oh3

Title

Crystal structure of a nitrate transporter

Components

Nitrate transporter 1.1

Keywords

membrane protein / tranport protein / Major Facilitator Superfamily / nitrate transporter / membrane

Function / homology

Function and homology information

basipetal auxin transport / nitrate transmembrane transport / nitrate transmembrane transporter activity / photoperiodism, flowering / response to nitrate / lateral root development / oligopeptide transport / auxin-activated signaling pathway / response to water deprivation / symporter activity ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.25 Å

Authors

Sun, J. / Bankston, J.R. / Payandeh, J. / Hinds, T.R. / Zagotta, W.N. / Zheng, N.

Citation

Journal: Nature / Year: 2014
Title: Crystal structure of the plant dual-affinity nitrate transporter NRT1.1.
Authors: Sun, J. / Bankston, J.R. / Payandeh, J. / Hinds, T.R. / Zagotta, W.N. / Zheng, N.

History

Deposition	Jan 16, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 12, 2014	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4oh3.cif.gz	414.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4oh3.ent.gz	357.9 KB	Display	PDB format
PDBx/mmJSON format	4oh3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4oh3_validation.pdf.gz	977.6 KB	Display	wwPDB validaton report
Full document	4oh3_full_validation.pdf.gz	1012.8 KB	Display
Data in XML	4oh3_validation.xml.gz	40.3 KB	Display
Data in CIF	4oh3_validation.cif.gz	54.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oh/4oh3 ftp://data.pdbj.org/pub/pdb/validation_reports/oh/4oh3	HTTPS FTP

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Related structure data

Similar structure data	5a2n-d 5a2o-d 3lcb-1 1nc4-d 4wb7-d 4crn-d 4twe-d 2h4t-d 3lzk-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	#208 - Apr 2017 Glucose Transporters similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Nitrate transporter 1.1

B: Nitrate transporter 1.1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	84.800, 188.465, 262.848
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Nitrate transporter 1.1 / AtNRT1 / Nitrate/chlorate transporter / Protein CHLORINA 1 Mass: 65807.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NRT1.1, CHL1, NRT1, At1g12110, F12F1.1, T28K15_13 / Plasmid: pFastBac / Cell line (production host): High Five / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q05085
#2: Sugar	ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₄H₄₆O₁₁ / Comment: detergent*YM
#3: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO₃

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.99 Å³/Da / Density % sol: 69.17 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M sodium acetate 30% PEG300 3% MPD, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.25→50 Å / Num. all: 34881 / Num. obs: 34573 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / R_merge(I) obs: 0.07 / Net I/σ(I): 1.2
Reflection shell	Resolution: 3.2→3.26 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.91 / Mean I/σ(I) obs: 1.4 / % possible all: 93.5

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.25→45.909 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 34.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3067	1461	4.86 %
R_work	0.2349	-	-
obs	0.2384	30085	89.5 %
all	-	33252	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.25→45.909 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7992	0	56	0	8048

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	8226
X-RAY DIFFRACTION	f_angle_d	1.454	11184
X-RAY DIFFRACTION	f_dihedral_angle_d	19.082	2812
X-RAY DIFFRACTION	f_chiral_restr	0.054	1347
X-RAY DIFFRACTION	f_plane_restr	0.006	1365

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 (%)
3.25-3.3661	0.2996	73	0.2829	1419	X-RAY DIFFRACTION	45
3.3661-3.5009	0.3646	102	0.2704	2107	X-RAY DIFFRACTION	67
3.5009-3.6601	0.3697	137	0.2596	2723	X-RAY DIFFRACTION	86
3.6601-3.853	0.3178	159	0.2623	3156	X-RAY DIFFRACTION	99
3.853-4.0943	0.3179	172	0.238	3146	X-RAY DIFFRACTION	100
4.0943-4.4102	0.3137	143	0.2217	3182	X-RAY DIFFRACTION	100
4.4102-4.8535	0.2959	165	0.2021	3191	X-RAY DIFFRACTION	100
4.8535-5.5548	0.2997	168	0.223	3205	X-RAY DIFFRACTION	100
5.5548-6.9945	0.3312	177	0.2752	3227	X-RAY DIFFRACTION	100
6.9945-45.9135	0.2697	165	0.2208	3268	X-RAY DIFFRACTION	97

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	2.9646	1.9413	-1.9202	3.7524	2.9877	8.5895	-0.2613	0.7082	-0.4565	-0.1664	0.3302	0.4297	-0.2296	0.5491	-0.081	1.5784	0.4497	-0.0143	1.2267	0.2326	0.6301	30.2788	24.7329	-62.3161
2	0.4441	-1.2042	0.2687	4.473	-1.6918	2.801	0.1896	0.4888	0.0284	-0.4073	-0.5732	0.2366	0.2544	0.0121	0.1046	0.4692	0.3682	-0.0568	0.8216	0.0932	0.3481	26.2113	14.2829	-30.6609
3	6.3091	0.7235	7.3656	1.627	1.2034	8.6782	0.4085	0.1595	-0.252	1.4095	0.3886	0.4597	0.9074	-1.1117	-0.6279	1.1673	0.1516	0.1777	1.0723	0.2447	0.5179	25.4867	10.0946	-3.7984
4	2.5459	-1.403	0.1854	2.4261	-0.3153	2.3441	0.0533	0.4083	0.0812	-0.2037	0.0564	0.1915	0.8403	0.2284	-0.498	0.6591	0.7343	-0.1943	0.7999	0.2331	0.5238	24.9105	14.5514	-35.5812
5	2.9262	-0.7052	0.4162	2.4956	-0.2936	2.3481	0.5071	0.7062	-0.0983	-0.8511	-0.3691	-0.3427	-0.3851	0.1791	-0.0002	0.9188	0.4722	0.0597	0.7961	0.161	0.5404	33.3639	15.6361	-40.7741
6	2.1125	0.5478	-1.4716	2.9552	0.4917	1.2963	0.251	0.8332	-0.4562	-0.2832	0.0077	-0.1891	0.2162	0.4922	-0.0922	0.3128	0.2715	-0.0428	0.7468	0.0142	0.468	33.1073	-3.1088	-35.5534
7	4.2932	3.6828	-3.0633	3.6499	-2.3391	2.3601	0.3305	1.9636	-0.2472	-0.3849	-0.5137	-1.3403	-0.254	0.3718	0.5192	0.9106	0.6663	-0.0515	1.5296	0.0289	0.8389	48.4369	-9.54	-48.5777
8	0.9994	-0.1964	-0.3347	1.3766	-0.2548	3.1052	0.1876	-0.3556	-0.5637	0.208	0.001	-0.2655	0.6794	0.6492	0.7279	0.6689	0.604	-0.3652	0.4881	0.2098	0.6312	41.0171	-9.4863	-18.9727
9	2.1476	0.8104	1.6935	5.1291	0.7983	7.4497	0.3127	0.0692	-0.6311	-0.55	-0.0947	0.1458	0.6816	-0.5932	-0.2242	0.468	0.2167	-0.0805	0.5479	0.0649	0.637	31.6168	-8.621	-31.2969
10	2.5827	0.2262	2.025	3.4688	2.724	7.024	-0.5237	0.6108	0.0514	-0.3006	0.25	1.5292	0.337	0.5957	0.3763	1.2607	0.3232	-0.2067	0.67	0.2181	0.9201	9.8985	31.6393	-42.7474
11	3.4762	-0.0822	0.9114	5.2921	1.1914	2.1742	-0.2441	0.0337	0.6042	0.8682	-0.0716	-0.3455	0.0925	0.3877	0.267	0.7018	0.2794	-0.0049	0.6185	0.0838	0.599	27.742	43.4154	-30.4972
12	2.5335	0.569	-1.4767	4.9998	-0.5147	1.4255	-0.3266	0.1975	0.7232	-0.6457	-0.1458	-0.0931	-0.9566	-0.5203	0.5675	0.7561	0.4874	0.0392	0.5063	0.2938	0.5748	24.7961	41.1562	-34.2721
13	1.8043	-0.609	0.6667	3.6794	-2.0261	3.3424	-0.0883	0.3087	0.1159	0.0707	0.0414	0.3579	-0.2964	-0.0498	0.1259	0.5041	0.3335	-0.052	0.6701	0.0199	0.6585	14.5194	42.4962	-45.7146
14	3.0144	-1.5818	-1.194	2.7064	0.1544	3.3494	-0.3032	-0.067	0.2525	0.4622	-0.2343	0.2575	-0.3188	-0.7463	0.5226	0.8718	0.394	-0.05	0.7081	-0.0082	0.8149	9.3455	59.153	-33.7547
15	2.682	-1.394	-3.2288	2.0015	5.1817	5.1889	0.2057	-0.3958	1.436	-0.6699	1.0307	0.4121	-1.3636	-0.4933	-1.4074	1.7981	0.4116	-0.3974	0.9027	-0.0979	0.9018	16.8728	64.9037	-8.0779
16	1.654	-0.0662	-0.9442	0.6184	-0.682	2.2602	-0.2437	-0.1904	0.886	0.0177	-0.0298	0.2322	-0.1228	0.0134	0.2442	0.9858	0.5343	0.0338	0.7383	0.036	0.9484	18.9758	60.4672	-33.5316
17	4.8932	1.0119	3.5947	2.2676	1.9703	4.4705	-1.0866	0.6369	1.5076	-0.0515	-0.1769	-0.1484	-1.528	0.846	1.0245	1.1036	0.0009	-0.2674	0.5246	0.1361	1.161	11.8867	70.4891	-46.4196
18	2	2	2	2	2	2	1.7276	-8.2707	-3.3721	-4.3121	-0.6351	13.5484	0.9529	0.8274	-1.0784	1.3894	0.1298	0.6025	1.2261	0.3892	1.3659	4.7644	65.4448	-75.1279

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 9:27 )	A	9 - 27
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 28:128 )	A	28 - 128
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 129:142 )	A	129 - 142
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 143:177 )	A	143 - 177
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 178:263 )	A	178 - 263
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 264:403 )	A	264 - 403
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 404:421 )	A	404 - 421
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 422:460 )	A	422 - 460
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 461:576 )	A	461 - 576
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 9:57 )	B	9 - 57
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 58:136 )	B	58 - 136
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 137:177 )	B	137 - 177
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 178:328 )	B	178 - 328
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 329:443 )	B	329 - 443
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 444:463 )	B	444 - 463
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 464:542 )	B	464 - 542
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 543:580 )	B	543 - 580
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 581:581 )	B	581

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