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- PDB-5a2n: Crystal structure of the nitrate transporter NRT1.1 from Arabidop... -

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Basic information

Entry
Database: PDB / ID: 5a2n
TitleCrystal structure of the nitrate transporter NRT1.1 from Arabidopsis thaliana.
ComponentsPROTEIN NRT1/ PTR FAMILY 6.3
KeywordsTRANSPORT PROTEIN / TRANSPORTER / NITRATE / MAJOR FACILITATOR SUPERFAMILY / POT FAMILY / NRT1/PTR FAMILY / NPF FAMILY
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 ...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 / 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
Protein NRT1/ PTR FAMILY 6.3
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.7 Å
AuthorsParker, J.L. / Newstead, S.
CitationJournal: Nature / Year: 2014
Title: Molecular Basis of Nitrate Uptake by the Plant Nitrate Transporter Nrt1.1.
Authors: Parker, J.L. / Newstead, S.
History
DepositionMay 20, 2015Deposition site: PDBE / Processing site: PDBE
SupersessionJun 17, 2015ID: 4CL4
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN NRT1/ PTR FAMILY 6.3
B: PROTEIN NRT1/ PTR FAMILY 6.3


Theoretical massNumber of molelcules
Total (without water)129,9672
Polymers129,9672
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-21.8 kcal/mol
Surface area46300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.800, 124.030, 153.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9954, -0.04337, -0.08534), (-0.03695, -0.6483, 0.7605), (-0.08831, 0.7601, 0.6437)
Vector: 188.4, 1.895, 8.923)

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Components

#1: Protein PROTEIN NRT1/ PTR FAMILY 6.3 / ATNPF6.3 / NITRATE TRANSPORTER 1.1 / ATNRT1 / NITRATE/CHLORATE TRANSPORTER / PROTEIN CHLORINA 1 / NRT1.1


Mass: 64983.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Description: TAIR ABRC STOCKS / Plasmid: MODIFED PDDGFP2 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: Q05085

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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: 4.46 Å3/Da / Density % sol: 72 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 22 % PEG 400, 0.05 M SODIUM CITRATE PH 4.5, 0.07 M SODIUM CHLORIDE AND 1.5 % PEG 600 USING THE HANGING DROP VAPOR DIFFUSION TECHNIQUE AT 4 CELSIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 3.7→29.57 Å / Num. obs: 21870 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 89.14 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20
Reflection shellResolution: 3.7→3.76 Å / Redundancy: 4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.2 / % possible all: 86.3

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
SHELXSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.7→27.53 Å / Cor.coef. Fo:Fc: 0.6491 / Cor.coef. Fo:Fc free: 0.6767 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.676
RfactorNum. reflection% reflectionSelection details
Rfree0.3101 1105 5.06 %RANDOM
Rwork0.2775 ---
obs0.2792 21857 86.26 %-
Displacement parametersBiso mean: 81.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.5632 Å20 Å20 Å2
2---1.8867 Å20 Å2
3----1.6765 Å2
Refine analyzeLuzzati coordinate error obs: 1.063 Å
Refinement stepCycle: LAST / Resolution: 3.7→27.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7308 0 0 0 7308
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017634HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2610504HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2510SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes100HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1126HARMONIC5
X-RAY DIFFRACTIONt_it7634HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion25.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion998SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9300SEMIHARMONIC4
LS refinement shellResolution: 3.7→3.88 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2665 55 4.41 %
Rwork0.2595 1192 -
all0.2598 1247 -
obs--86.26 %
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)
13.03771.49150.72257.3263-3.27653.4988-0.0036-0.5416-0.48520.9198-0.4914-0.13250.7729-0.22780.495-0.9666-0.4360.6066-0.37790.0855-0.669687.984916.676469.8096
201.1933-0.31793.0027-1.56170.7057-0.0453-0.241-0.91710.1927-0.2432-0.34190.7202-0.65690.28850.3364-0.30.3801-0.55840.2046-0.092685.8239-5.689574.1864
30.20665.283-3.64058.7142-3.96654.2712-0.07310.02130.1732-0.5911-1.0239-1.0382-0.70380.88381.0969-0.803-0.3597-0.0929-0.3928-0.0984-0.676295.697638.73856.0828
40.26011.0226-2.32175.3653-1.88710.11530.02680.11770.63260.0934-0.0833-0.7183-0.35020.47130.05640.3235-0.4646-0.1395-0.59110.5414-0.641396.930458.824744.7897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|21 - A|269 }
2X-RAY DIFFRACTION2{ A|326 - A|573 }
3X-RAY DIFFRACTION3{ B|21 - B|229 }
4X-RAY DIFFRACTION4{ B|326 - B|573 }

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