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- PDB-5bz3: CRYSTAL STRUCTURE OF SODIUM PROTON ANTIPORTER NAPA IN OUTWARD-FAC... -

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Basic information

Entry
Database: PDB / ID: 5bz3
TitleCRYSTAL STRUCTURE OF SODIUM PROTON ANTIPORTER NAPA IN OUTWARD-FACING CONFORMATION.
ComponentsNa(+)/H(+) antiporter
KeywordsTRANSPORT PROTEIN / HIGH PH / OUTWARD-CONFORMATION / LCP
Function / homology
Function and homology information


antiporter activity / sodium ion transport / proton transmembrane transport / metal ion binding / identical protein binding / membrane
Similarity search - Function
Na+/H+ antiporter like fold - #20 / Na+/H+ antiporter like fold / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE / Na(+)/H(+) antiporter / Na(+)/H(+) antiporter
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsCoincon, M. / Uzdavinys, P. / Emmanuel, N. / Cameron, A. / Drew, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters.
Authors: Coincon, M. / Uzdavinys, P. / Nji, E. / Dotson, D.L. / Winkelmann, I. / Abdul-Hussein, S. / Cameron, A.D. / Beckstein, O. / Drew, D.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Structure summary
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Mar 9, 2016Group: Database references
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Na(+)/H(+) antiporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2578
Polymers40,1541
Non-polymers2,1037
Water1,36976
1
A: Na(+)/H(+) antiporter
hetero molecules

A: Na(+)/H(+) antiporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,51416
Polymers80,3082
Non-polymers4,20614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4120 Å2
ΔGint-45 kcal/mol
Surface area31370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.580, 94.090, 147.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-533-

HOH

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Components

#1: Protein Na(+)/H(+) antiporter


Mass: 40153.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TT_C1108 / Plasmid: PWALDOGFPE / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: Q72IM4, UniProt: Q5SIA2*PLUS
#2: Chemical
ChemComp-7E8 / (2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE / 7.7 MAG


Mass: 300.434 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C17H32O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.4
Details: Lipid: MAG 7.7 (Lot: 141MG(7.7)-15, Avanti) protein (30mg/ml) weight ratio 1:1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→47 Å / Num. obs: 17750 / % possible obs: 100 % / Observed criterion σ(I): 12.24 / Redundancy: 4.5 % / CC1/2: 0.972 / Rmerge(I) obs: 0.182 / Net I/σ(I): 12.24
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.036 / Mean I/σ(I) obs: 1.65 / CC1/2: 0.735 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1938refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 2.3→47 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 877 4.94 %Random selection
Rwork0.2059 ---
obs0.2065 17750 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 147 76 3045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053017
X-RAY DIFFRACTIONf_angle_d0.9584068
X-RAY DIFFRACTIONf_dihedral_angle_d16.2151106
X-RAY DIFFRACTIONf_chiral_restr0.051508
X-RAY DIFFRACTIONf_plane_restr0.004493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.44410.25931460.24672760X-RAY DIFFRACTION99
2.4441-2.63280.24331370.22052791X-RAY DIFFRACTION100
2.6328-2.89770.22731210.19922801X-RAY DIFFRACTION99
2.8977-3.31690.22441490.19952787X-RAY DIFFRACTION100
3.3169-4.17860.18791470.18912840X-RAY DIFFRACTION99
4.1786-48.4990.22091770.21072894X-RAY DIFFRACTION98

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