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- PDB-4jr9: Crystal structure of nitrate/nitrite exchanger NarK -

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Basic information

Entry
Database: PDB / ID: 4jr9
TitleCrystal structure of nitrate/nitrite exchanger NarK
Components
  • Immunoglobulin Gamma-2a, Heavy chain
  • Immunoglobulin Kappa, Light chain
  • Nitrite extrusion protein 1
KeywordsTRANSPORT PROTEIN/Immune System / Transporter / Immunoglobulin / Major Facilitator Superfamily / Exchanger / TRANSPORT PROTEIN-Immune System complex
Function / homology
Function and homology information


nitrite transmembrane transporter activity / nitrite transport / nitrate transmembrane transporter activity / nitrate transmembrane transport / nitrate catabolic process / solute:inorganic anion antiporter activity / nitrate assimilation / plasma membrane
Similarity search - Function
Nitrate transporter NarK/NarU-like / Nitrate transporter / MFS general substrate transporter like domains / Growth Hormone; Chain: A; / Major facilitator superfamily / Major Facilitator Superfamily / MFS transporter superfamily / Immunoglobulins / Up-down Bundle / Immunoglobulin-like ...Nitrate transporter NarK/NarU-like / Nitrate transporter / MFS general substrate transporter like domains / Growth Hormone; Chain: A; / Major facilitator superfamily / Major Facilitator Superfamily / MFS transporter superfamily / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
methyl alpha-D-glucopyranoside / Nitrate/nitrite antiporter NarK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZheng, H. / Wisedchaisri, G. / Gonen, T.
CitationJournal: Nature / Year: 2013
Title: Crystal structure of a nitrate/nitrite exchanger.
Authors: Zheng, H. / Wisedchaisri, G. / Gonen, T.
History
DepositionMar 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrite extrusion protein 1
H: Immunoglobulin Gamma-2a, Heavy chain
L: Immunoglobulin Kappa, Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6584
Polymers96,4643
Non-polymers1941
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.266, 86.545, 144.789
Angle α, β, γ (deg.)90.00, 115.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 50009.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1223, JW1214, narK / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) C41 / References: UniProt: P10903
#2: Antibody Immunoglobulin Gamma-2a, Heavy chain


Mass: 23188.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma
#3: Antibody Immunoglobulin Kappa, Light chain


Mass: 23265.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma
#4: Sugar ChemComp-GYP / methyl alpha-D-glucopyranoside / METHYL-ALPHA-D-GLUCOPYRANOSIDE / ALPHA-METHYL-D-GLUCOPYRANOSIDE / methyl alpha-D-glucoside / methyl D-glucoside / methyl glucoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DGlcp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-glucopyranoseCOMMON NAMEGMML 1.0
methyl-a-D-glucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
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: 4.06 Å3/Da / Density % sol: 69.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 28% PEG400, 0.1 M citric acid pH 3.5, 0.1M NaCl, 0.1M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999973 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999973 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 47606 / % possible obs: 99.5 % / Observed criterion σ(I): 1.5 / Redundancy: 7.1 % / Biso Wilson estimate: 65 Å2 / Rsym value: 0.097 / Net I/σ(I): 19.8
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 2237 / Rsym value: 0.892 / % possible all: 93.2

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Processing

Software
NameVersionClassification
BOSdata collection
PHASER2.3.0phasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3TT1, 1F8T, 3TT3, 1MRC

3tt1

1f8t

3tt3

1mrc


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.892 / SU B: 8.75 / SU ML: 0.187 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.344 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: A strong density on the surface of NarK is likely from the sugar head group of the decylmaltoside detergent used during protein purification and is modelled in the structure as maltose.
RfactorNum. reflection% reflectionSelection details
Rfree0.26132 2408 5.1 %RANDOM
Rwork0.22889 ---
obs0.23054 45063 99.45 %-
all-47471 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.779 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å20 Å2-0.56 Å2
2---1.3 Å20 Å2
3---3.26 Å2
Refine analyzeLuzzati coordinate error obs: 0.366 Å
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6273 0 13 45 6331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.026462
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9468807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7075829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60423.174230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.70715962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5061523
X-RAY DIFFRACTIONr_chiral_restr0.0860.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214832
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 150 -
Rwork0.344 3056 -
obs-3056 94.82 %

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