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- PDB-4iu9: Crystal structure of a membrane transporter -

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Basic information

Entry
Database: PDB / ID: 4iu9
TitleCrystal structure of a membrane transporter
ComponentsNitrite extrusion protein 2
KeywordsTRANSPORT PROTEIN / membrane protein / nitrate-nitrite porter family transporter / MFS fold
Function / homology
Function and homology information


nitrite transmembrane transporter activity / nitrate transmembrane transporter activity / nitrate assimilation / plasma membrane
Similarity search - Function
Nitrate transporter NarK/NarU-like / Nitrate transporter / MFS general substrate transporter like domains / Major facilitator superfamily / Major Facilitator Superfamily / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Nitrate/nitrite transporter NarU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.005 Å
AuthorsYan, H. / Huang, W. / Yan, C. / Gong, X. / Jiang, S. / Zhao, Y. / Wang, J. / Shi, Y.
CitationJournal: Cell Rep / Year: 2013
Title: Structure and mechanism of a nitrate transporter.
Authors: Yan, H. / Huang, W. / Yan, C. / Gong, X. / Jiang, S. / Zhao, Y. / Wang, J. / Shi, Y.
History
DepositionJan 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Nitrite extrusion protein 2
A: Nitrite extrusion protein 2


Theoretical massNumber of molelcules
Total (without water)101,3072
Polymers101,3072
Non-polymers00
Water00
1
B: Nitrite extrusion protein 2


Theoretical massNumber of molelcules
Total (without water)50,6541
Polymers50,6541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Nitrite extrusion protein 2


Theoretical massNumber of molelcules
Total (without water)50,6541
Polymers50,6541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.439, 118.211, 127.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nitrite extrusion protein 2 / Nitrite facilitator 2


Mass: 50653.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: narU / Production host: Escherichia coli (E. coli) / References: UniProt: P37758

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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: 4.42 Å3/Da / Density % sol: 72.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl (pH 8.5), 33% (w/v) PEG 400 and 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.07082 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07082 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. all: 35777 / Num. obs: 30017 / % possible obs: 83.9 % / Observed criterion σ(I): -3
Reflection shellResolution: 3→3.11 Å / % possible all: 62.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IU8

4iu8


Resolution: 3.005→39.84 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 39.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3163 1407 5.16 %RANDOM
Rwork0.2608 ---
obs0.2638 27288 75.98 %-
all-35777 --
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 84.45 Å2 / ksol: 0.286 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-102.4276 Å2-0 Å2-0 Å2
2---30.5286 Å20 Å2
3----71.899 Å2
Refinement stepCycle: LAST / Resolution: 3.005→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6061 0 0 0 6061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096232
X-RAY DIFFRACTIONf_angle_d1.2838502
X-RAY DIFFRACTIONf_dihedral_angle_d17.0152015
X-RAY DIFFRACTIONf_chiral_restr0.085996
X-RAY DIFFRACTIONf_plane_restr0.0061056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0047-3.11210.399570.30371043X-RAY DIFFRACTION31
3.1121-3.23660.3985700.29781425X-RAY DIFFRACTION43
3.2366-3.38380.3513990.28211886X-RAY DIFFRACTION56
3.3838-3.56210.331220.26432243X-RAY DIFFRACTION67
3.5621-3.78520.37661480.26532686X-RAY DIFFRACTION80
3.7852-4.07720.36161700.27013168X-RAY DIFFRACTION94
4.0772-4.4870.27321800.21963368X-RAY DIFFRACTION99
4.487-5.13510.25191870.20493396X-RAY DIFFRACTION99
5.1351-6.46520.33611930.27423384X-RAY DIFFRACTION99
6.4652-39.84390.31811810.29373282X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -0.4538 Å / Origin y: -1.0669 Å / Origin z: -17.9241 Å
111213212223313233
T1.3314 Å2-0.0929 Å2-0.0027 Å2-0.9815 Å2-0.0109 Å2--1.094 Å2
L0.5084 °2-0.2264 °20.3666 °2-0.0333 °2-0.225 °2--0.6863 °2
S0.0476 Å °-0.0121 Å °0.0518 Å °0.0955 Å °-0.0561 Å °-0.012 Å °-0.0043 Å °-0.0139 Å °0.0031 Å °
Refinement TLS groupSelection details: all

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