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- PDB-4u4t: Structure of a nitrate/nitrite antiporter NarK in nitrate-bound i... -

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Basic information

Entry
Database: PDB / ID: 4u4t
TitleStructure of a nitrate/nitrite antiporter NarK in nitrate-bound inward-open 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,52710
Polymers51,0521
Non-polymers2,4759
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-32 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.394, 109.358, 126.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nitrate/nitrite transporter NarK / Nitrite extrusion protein 1 / Nitrite facilitator 1


Mass: 51052.461 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 40 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 32-36% PEG 400, 10 mM zinc acetate, 3% D-sucrose, 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 MX-225 / Detector: CCD / Date: Dec 18, 2011
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: 19921 / % possible obs: 99.8 % / Redundancy: 6.4 % / Net I/σ(I): 6.79

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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→41.3 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 998 5.01 %
Rwork0.217 --
obs0.2185 19921 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→41.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 77 31 3400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093453
X-RAY DIFFRACTIONf_angle_d1.1694674
X-RAY DIFFRACTIONf_dihedral_angle_d14.6991159
X-RAY DIFFRACTIONf_chiral_restr0.047531
X-RAY DIFFRACTIONf_plane_restr0.006575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.52660.32141400.29112654X-RAY DIFFRACTION100
2.5266-2.68490.32921390.26252631X-RAY DIFFRACTION100
2.6849-2.89220.25331400.24842672X-RAY DIFFRACTION100
2.8922-3.18310.2671410.23962684X-RAY DIFFRACTION100
3.1831-3.64350.27351420.21442681X-RAY DIFFRACTION100
3.6435-4.58950.231440.19092729X-RAY DIFFRACTION100
4.5895-41.30640.20611520.19632872X-RAY DIFFRACTION100
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)
10.2115-0.13680.07630.1390.0360.1566-0.10030.2319-0.0061-0.3411-0.1984-0.1655-0.11970.1457-0.00020.5411-0.00060.05230.4960.05330.3811-5.4538-3.148711.2076
20.82020.044-0.46061.65360.18431.05880.04490.00030.0963-0.0744-0.08630.0021-0.1233-0.020500.279-0.00070.00160.3499-0.01230.3468-12.218-8.344232.1149
30.1956-0.0049-0.03980.26230.05020.0162-0.1797-0.2238-0.40140.2637-0.0365-0.09150.129-0.155-0.00020.56230.0194-0.01770.3945-0.03260.5395-10.8342-32.919936.1812
40.7772-0.1769-0.10730.97020.22730.13260.13320.138-0.18-0.3154-0.06560.15310.4483-0.1017-0.00020.5095-0.04060.00620.4444-0.06310.435-18.8173-25.797622.411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 316 )
3X-RAY DIFFRACTION3chain 'A' and (resid 317 through 348 )
4X-RAY DIFFRACTION4chain 'A' and (resid 349 through 464 )

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