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- PDB-4oh3: Crystal structure of a nitrate transporter -

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Basic information

Entry
Database: PDB / ID: 4oh3
TitleCrystal structure of a nitrate transporter
ComponentsNitrate transporter 1.1
Keywordsmembrane protein / tranport protein / Major Facilitator Superfamily / nitrate transporter / membrane
Function / homology
Function and homology information


nitrate transmembrane transport / basipetal auxin 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 ...nitrate transmembrane transport / basipetal auxin 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 / response to herbicide / nitrate assimilation / plasma membrane
Similarity search - Function
PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Protein NRT1/ PTR FAMILY 6.3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.25 Å
AuthorsSun, J. / Bankston, J.R. / Payandeh, J. / Hinds, T.R. / Zagotta, W.N. / Zheng, N.
CitationJournal: 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
DepositionJan 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrate transporter 1.1
B: Nitrate transporter 1.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,7606
Polymers131,6152
Non-polymers1,1454
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-32 kcal/mol
Surface area47520 Å2
MethodPISA
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 number20
Space group name H-MC2221

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Components

#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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.99 Å3/Da / Density % sol: 69.17 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 1.2
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.4 / % possible all: 93.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.3067 1461 4.86 %
Rwork0.2349 --
obs0.2384 30085 89.5 %
all-33252 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→45.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7992 0 56 0 8048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018226
X-RAY DIFFRACTIONf_angle_d1.45411184
X-RAY DIFFRACTIONf_dihedral_angle_d19.0822812
X-RAY DIFFRACTIONf_chiral_restr0.0541347
X-RAY DIFFRACTIONf_plane_restr0.0061365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.36610.2996730.28291419X-RAY DIFFRACTION45
3.3661-3.50090.36461020.27042107X-RAY DIFFRACTION67
3.5009-3.66010.36971370.25962723X-RAY DIFFRACTION86
3.6601-3.8530.31781590.26233156X-RAY DIFFRACTION99
3.853-4.09430.31791720.2383146X-RAY DIFFRACTION100
4.0943-4.41020.31371430.22173182X-RAY DIFFRACTION100
4.4102-4.85350.29591650.20213191X-RAY DIFFRACTION100
4.8535-5.55480.29971680.2233205X-RAY DIFFRACTION100
5.5548-6.99450.33121770.27523227X-RAY DIFFRACTION100
6.9945-45.91350.26971650.22083268X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.96461.9413-1.92023.75242.98778.5895-0.26130.7082-0.4565-0.16640.33020.4297-0.22960.5491-0.0811.57840.4497-0.01431.22670.23260.630130.278824.7329-62.3161
20.4441-1.20420.26874.473-1.69182.8010.18960.48880.0284-0.4073-0.57320.23660.25440.01210.10460.46920.3682-0.05680.82160.09320.348126.211314.2829-30.6609
36.30910.72357.36561.6271.20348.67820.40850.1595-0.2521.40950.38860.45970.9074-1.1117-0.62791.16730.15160.17771.07230.24470.517925.486710.0946-3.7984
42.5459-1.4030.18542.4261-0.31532.34410.05330.40830.0812-0.20370.05640.19150.84030.2284-0.4980.65910.7343-0.19430.79990.23310.523824.910514.5514-35.5812
52.9262-0.70520.41622.4956-0.29362.34810.50710.7062-0.0983-0.8511-0.3691-0.3427-0.38510.1791-0.00020.91880.47220.05970.79610.1610.540433.363915.6361-40.7741
62.11250.5478-1.47162.95520.49171.29630.2510.8332-0.4562-0.28320.0077-0.18910.21620.4922-0.09220.31280.2715-0.04280.74680.01420.46833.1073-3.1088-35.5534
74.29323.6828-3.06333.6499-2.33912.36010.33051.9636-0.2472-0.3849-0.5137-1.3403-0.2540.37180.51920.91060.6663-0.05151.52960.02890.838948.4369-9.54-48.5777
80.9994-0.1964-0.33471.3766-0.25483.10520.1876-0.3556-0.56370.2080.001-0.26550.67940.64920.72790.66890.604-0.36520.48810.20980.631241.0171-9.4863-18.9727
92.14760.81041.69355.12910.79837.44970.31270.0692-0.6311-0.55-0.09470.14580.6816-0.5932-0.22420.4680.2167-0.08050.54790.06490.63731.6168-8.621-31.2969
102.58270.22622.0253.46882.7247.024-0.52370.61080.0514-0.30060.251.52920.3370.59570.37631.26070.3232-0.20670.670.21810.92019.898531.6393-42.7474
113.4762-0.08220.91145.29211.19142.1742-0.24410.03370.60420.8682-0.0716-0.34550.09250.38770.2670.70180.2794-0.00490.61850.08380.59927.74243.4154-30.4972
122.53350.569-1.47674.9998-0.51471.4255-0.32660.19750.7232-0.6457-0.1458-0.0931-0.9566-0.52030.56750.75610.48740.03920.50630.29380.574824.796141.1562-34.2721
131.8043-0.6090.66673.6794-2.02613.3424-0.08830.30870.11590.07070.04140.3579-0.2964-0.04980.12590.50410.3335-0.0520.67010.01990.658514.519442.4962-45.7146
143.0144-1.5818-1.1942.70640.15443.3494-0.3032-0.0670.25250.4622-0.23430.2575-0.3188-0.74630.52260.87180.394-0.050.7081-0.00820.81499.345559.153-33.7547
152.682-1.394-3.22882.00155.18175.18890.2057-0.39581.436-0.66991.03070.4121-1.3636-0.4933-1.40741.79810.4116-0.39740.9027-0.09790.901816.872864.9037-8.0779
161.654-0.0662-0.94420.6184-0.6822.2602-0.2437-0.19040.8860.0177-0.02980.2322-0.12280.01340.24420.98580.53430.03380.73830.0360.948418.975860.4672-33.5316
174.89321.01193.59472.26761.97034.4705-1.08660.63691.5076-0.0515-0.1769-0.1484-1.5280.8461.02451.10360.0009-0.26740.52460.13611.16111.886770.4891-46.4196
182222221.7276-8.2707-3.3721-4.3121-0.635113.54840.95290.8274-1.07841.38940.12980.60251.22610.38921.36594.764465.4448-75.1279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:27 )A9 - 27
2X-RAY DIFFRACTION2( CHAIN A AND RESID 28:128 )A28 - 128
3X-RAY DIFFRACTION3( CHAIN A AND RESID 129:142 )A129 - 142
4X-RAY DIFFRACTION4( CHAIN A AND RESID 143:177 )A143 - 177
5X-RAY DIFFRACTION5( CHAIN A AND RESID 178:263 )A178 - 263
6X-RAY DIFFRACTION6( CHAIN A AND RESID 264:403 )A264 - 403
7X-RAY DIFFRACTION7( CHAIN A AND RESID 404:421 )A404 - 421
8X-RAY DIFFRACTION8( CHAIN A AND RESID 422:460 )A422 - 460
9X-RAY DIFFRACTION9( CHAIN A AND RESID 461:576 )A461 - 576
10X-RAY DIFFRACTION10( CHAIN B AND RESID 9:57 )B9 - 57
11X-RAY DIFFRACTION11( CHAIN B AND RESID 58:136 )B58 - 136
12X-RAY DIFFRACTION12( CHAIN B AND RESID 137:177 )B137 - 177
13X-RAY DIFFRACTION13( CHAIN B AND RESID 178:328 )B178 - 328
14X-RAY DIFFRACTION14( CHAIN B AND RESID 329:443 )B329 - 443
15X-RAY DIFFRACTION15( CHAIN B AND RESID 444:463 )B444 - 463
16X-RAY DIFFRACTION16( CHAIN B AND RESID 464:542 )B464 - 542
17X-RAY DIFFRACTION17( CHAIN B AND RESID 543:580 )B543 - 580
18X-RAY DIFFRACTION18( CHAIN B AND RESID 581:581 )B581

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