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- PDB-4iu8: Crystal structure of a membrane transporter (selenomethionine der... -

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Basic information

Entry
Database: PDB / ID: 4iu8
TitleCrystal structure of a membrane transporter (selenomethionine derivative)
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 ION / Nitrate/nitrite transporter NarU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.11 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)102,7763
Polymers102,7142
Non-polymers621
Water0
1
A: Nitrite extrusion protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4192
Polymers51,3571
Non-polymers621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nitrite extrusion protein 2


Theoretical massNumber of molelcules
Total (without water)51,3571
Polymers51,3571
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.582, 117.501, 127.411
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: 51357.055 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
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / 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: 3.94 Å3/Da / Density % sol: 68.78 %
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: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. all: 29391 / Num. obs: 24453 / % possible obs: 83.2 % / Observed criterion σ(I): -3
Reflection shellResolution: 3.1→3.21 Å / % possible all: 34.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.11→40 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.83 / SU B: 19.094 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R Free: 0.521 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29885 1224 5 %RANDOM
Rwork0.23853 ---
obs0.24158 23188 82.68 %-
all-29391 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.692 Å2
Baniso -1Baniso -2Baniso -3
1-14.72 Å20 Å20 Å2
2---1.15 Å20 Å2
3----13.57 Å2
Refinement stepCycle: LAST / Resolution: 3.11→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6210 0 4 0 6214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196383
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.958711
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6425843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.03822.683205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.56415792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3621516
X-RAY DIFFRACTIONr_chiral_restr0.1080.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214778
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.108→3.188 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 25 -
Rwork0.285 596 -
obs--30.04 %

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