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- PDB-5a2o: Crystal structure of the nitrate transporter NRT1.1 from Arabidop... -

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Basic information

Entry
Database: PDB / ID: 5a2o
TitleCrystal structure of the nitrate transporter NRT1.1 from Arabidopsis thaliana in complex with nitrate.
ComponentsNITRATE TRANSPORTER 1.1
KeywordsTRANSPORT PROTEIN / TRANSPORTER / NITRATE / MFS / POT FAMILY / NRT1/PTR FAMILY / NPF FAMILY / MFS TRANSPORTER
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
NITRATE ION / Protein NRT1/ PTR FAMILY 6.3
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.71 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: 4CL5
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 2.0Feb 27, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Experimental preparation / Other
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_PDB_rev / database_PDB_rev_record / diffrn_source / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
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 / _atom_site.pdbx_auth_atom_name / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_PDB_atom_name / _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)130,0914
Polymers129,9672
Non-polymers1242
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-18.8 kcal/mol
Surface area46150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.830, 123.590, 153.620
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: (-0.9959, -0.03848, -0.08137), (-0.0371, -0.6481, 0.7606), (-0.08201, 0.7606, 0.6441)
Vector: 188, 1.632, 8.475)

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Components

#1: Protein NITRATE TRANSPORTER 1.1


Mass: 64983.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Description: CLONED FROM TAIR ABRC STOCK CLONE U15475 / Plasmid: MODIFED PDDGFP2 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: Q05085
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3

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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: 3.71→27.74 Å / Num. obs: 22013 / % possible obs: 87.6 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 88.31 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.3
Reflection shellResolution: 3.71→3.89 Å / Redundancy: 3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.1 / % possible all: 87.6

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Processing

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

Resolution: 3.71→27.74 Å / Cor.coef. Fo:Fc: 0.6983 / Cor.coef. Fo:Fc free: 0.5841 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.711
Details: THE NITRATE MOLECULE WAS BETTER RESOLVED IN CHAIN A COMPARED TO CHAIN B. DURING REFINEMENT THE POSITION OF NITRATE IN THE BINDING SITE OF CHAIN B SHIFTS APPROX. 1.7 A COMPARED TO THE ...Details: THE NITRATE MOLECULE WAS BETTER RESOLVED IN CHAIN A COMPARED TO CHAIN B. DURING REFINEMENT THE POSITION OF NITRATE IN THE BINDING SITE OF CHAIN B SHIFTS APPROX. 1.7 A COMPARED TO THE POSITION IN CHAIN A. GIVEN THE ERROR IN REFINEMENT AT THIS RESOLUTION IT IS DIFFICULT TO ASCERTAIN THE SIGNIFICANCE OF THIS WITH RESPECT TO THE BINDING SITE. HOWEVER, THE NITRATE IS STILL POSITIONED CLOSE ENOUGH TO INTERACT WITH HIS356 IN CHAIN B, WHICH IS SHOWN BY THE BINDING AND TRANSPORT DATA IN THE ACCOMPANYING MANUSCRIPT TO PLAY AN IMPORTANT ROLE IN NITRATE BINDING.
RfactorNum. reflection% reflectionSelection details
Rfree0.3275 1121 5.09 %RANDOM
Rwork0.287 ---
obs0.2891 22013 87.65 %-
Displacement parametersBiso mean: 106.81 Å2
Baniso -1Baniso -2Baniso -3
1--5.3894 Å20 Å20 Å2
2--0.1222 Å20 Å2
3---5.2672 Å2
Refine analyzeLuzzati coordinate error obs: 1.15 Å
Refinement stepCycle: LAST / Resolution: 3.71→27.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7308 0 8 0 7316
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114032HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0724916HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3172SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes100HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2012HARMONIC5
X-RAY DIFFRACTIONt_it14032HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion20.15
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_contact16274SEMIHARMONIC4
LS refinement shellResolution: 3.71→3.89 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2118 54 4.06 %
Rwork0.2702 1275 -
all0.2679 1329 -
obs--87.65 %
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)
12.30160.5119-1.91579.0827-1.36072.5080.1061-0.5434-0.44540.8415-0.4723-0.24520.8875-0.07610.3663-1.0795-0.27630.5485-0.05010.0125-0.223388.069516.670369.9544
202.6231-0.77060.4178-2.13770.52740.0749-0.2472-0.52360.0038-0.3374-0.1936-0.0455-0.84070.26250.524-0.11540.3642-0.15040.02220.290683.9696-4.86774.3168
30.95164.3834-1.217710.3181-7.75514.7461-0.4164-0.2287-0.0126-0.395-0.6358-0.2589-1.12210.71441.0522-1.201-0.4917-0.10120.0787-0.0683-0.293995.396438.551756.1273
402.2693-1.92775.0896-2.1420.29680.0021-0.12680.23120.7791-0.3104-0.9167-0.21751.17330.30830.4873-0.4291-0.2416-0.11520.42-0.142498.427858.187345.7069
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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