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- PDB-4u4w: Structure of a nitrate/nitrite antiporter NarK in nitrate-bound o... -

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Basic information

Entry
Database: PDB / ID: 4u4w
TitleStructure of a nitrate/nitrite antiporter NarK in nitrate-bound occluded state
ComponentsNitrate/nitrite transporter NarK
KeywordsTRANSPORT PROTEIN / Transporter / Nitrate Nitrite Porter family / Major facilitator superfamily / Membrane transporter
Function / homology
Function and homology information


nitrite transmembrane transporter activity / nitrate transmembrane transport / nitrite transport / nitrate transmembrane transporter activity / 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 / Major facilitator superfamily / Major Facilitator Superfamily / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Nitrate/nitrite antiporter NarK
Similarity search - Component
Biological speciesEscherichia coli str. K12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFukuda, M. / Takeda, H. / Kato, H.E. / Doki, S. / Ito, K. / Maturana, A.D. / Ishitani, R. / Nureki, O.
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK
Authors: Fukuda, M. / Takeda, H. / Kato, H.E. / Doki, S. / Ito, K. / Maturana, A.D. / Ishitani, R. / Nureki, O.
History
DepositionJul 24, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrate/nitrite transporter NarK
B: Nitrate/nitrite transporter NarK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,83619
Polymers102,1052
Non-polymers4,73117
Water1,874104
1
A: Nitrate/nitrite transporter NarK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,59610
Polymers51,0521
Non-polymers2,5449
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nitrate/nitrite transporter NarK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2409
Polymers51,0521
Non-polymers2,1878
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.780, 86.100, 221.550
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 Nitrate/nitrite transporter NarK / Nitrite extrusion protein 1 / Nitrite facilitator 1


Mass: 51052.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. MG1655 (bacteria)
Strain: MG1655 / Gene: narK, b1223, JW1214 / Plasmid: pET variant / Production host: Escherichia coli (E. coli) / References: UniProt: P10903
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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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: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.8
Details: 31% PEG 500DME, 100 mM ammonium nitrate, 100 mM MES-NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 50895 / % possible obs: 97.2 % / Redundancy: 4.2 % / Net I/σ(I): 7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.3_1479) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.35 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 1766 3.47 %
Rwork0.2191 --
obs0.2198 50895 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6486 0 224 104 6814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026873
X-RAY DIFFRACTIONf_angle_d0.6719267
X-RAY DIFFRACTIONf_dihedral_angle_d11.6622367
X-RAY DIFFRACTIONf_chiral_restr0.0211041
X-RAY DIFFRACTIONf_plane_restr0.0031130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.46490.38161360.35763780X-RAY DIFFRACTION98
2.4649-2.53740.32031350.30823765X-RAY DIFFRACTION99
2.5374-2.61930.29111350.29383766X-RAY DIFFRACTION98
2.6193-2.71290.32021340.26713752X-RAY DIFFRACTION98
2.7129-2.82150.26131370.25713764X-RAY DIFFRACTION98
2.8215-2.94990.28421350.2533768X-RAY DIFFRACTION98
2.9499-3.10540.2671360.24143775X-RAY DIFFRACTION98
3.1054-3.30.27341360.22923784X-RAY DIFFRACTION98
3.3-3.55470.24611360.20853771X-RAY DIFFRACTION97
3.5547-3.91230.19341350.1893758X-RAY DIFFRACTION97
3.9123-4.4780.20831350.19053780X-RAY DIFFRACTION96
4.478-5.64050.18961370.1923793X-RAY DIFFRACTION95
5.6405-48.35950.21221390.1923873X-RAY DIFFRACTION93
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)
10.84550.3529-0.22090.73150.02381.5258-0.06840.0508-0.1104-0.0289-0.0121-0.03880.10150.0043-00.46070.02530.00770.3689-0.0220.4454-3.3174-36.8661-28.5992
20.4282-0.04410.18811.055-0.46641.73480.0124-0.02640.05090.1851-0.0512-0.0618-0.3567-0.045-0.00010.4684-0.0306-0.0280.45870.01210.446914.3368-1.0953-27.0401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 11:457 or chain A and resseq 501:501
2X-RAY DIFFRACTION2chain B and resseq 12:458 or chain B and resseq 501:501

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