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- PDB-5bz2: CRYSTAL STRUCTURE OF THE SODIUM PROTON ANTIPORTER NAPA IN INWARD-... -

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Basic information

Entry
Database: PDB / ID: 5bz2
TitleCRYSTAL STRUCTURE OF THE SODIUM PROTON ANTIPORTER NAPA IN INWARD-FACING CONFORMATION
ComponentsNa(+)/H(+) antiporter
KeywordsTRANSPORT PROTEIN / INWARD-FACING / CYSTEIN CROSSLINK
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
Na(+)/H(+) antiporter / Na(+)/H(+) antiporter
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsCoincon, M. / Uzdavinys, P. / 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: Database references / Structure summary
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Mar 9, 2016Group: Database references
Revision 1.5Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 6, 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: Na(+)/H(+) antiporter


Theoretical massNumber of molelcules
Total (without water)40,3061
Polymers40,3061
Non-polymers00
Water00
1
A: Na(+)/H(+) antiporter

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


Theoretical massNumber of molelcules
Total (without water)80,6122
Polymers80,6122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3560 Å2
ΔGint-42 kcal/mol
Surface area31710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.710, 84.640, 201.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 40306.109 Da / Num. of mol.: 1 / Mutation: V31C I130C
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
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: 4.14 Å3/Da / Density % sol: 70.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.05M glycine pH 9.5, 0.1M NaCl, 34-38% PEG 300 / PH range: 9.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 3.7→33.64 Å / Num. obs: 7404 / % possible obs: 100 % / Observed criterion σ(I): 13.26 / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.26
Reflection shellResolution: 3.7→3.832 Å / Redundancy: 13.3 % / Rmerge(I) obs: 2.788 / Mean I/σ(I) obs: 1.13 / CC1/2: 0.575 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2006: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bwz

4bwz


Resolution: 3.7→33.64 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 0.48 / Phase error: 36.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3285 1365 9.98 %Random selection
Rwork0.2904 ---
obs0.2937 13684 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→33.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 0 0 2823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052871
X-RAY DIFFRACTIONf_angle_d0.8363910
X-RAY DIFFRACTIONf_dihedral_angle_d14.7061006
X-RAY DIFFRACTIONf_chiral_restr0.05499
X-RAY DIFFRACTIONf_plane_restr0.004484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7001-3.83210.43971580.40381245X-RAY DIFFRACTION100
3.8321-3.98530.41411360.36741189X-RAY DIFFRACTION100
3.9853-4.16640.32261490.33921237X-RAY DIFFRACTION100
4.1664-4.38560.33021500.32441229X-RAY DIFFRACTION100
4.3856-4.65970.32821680.31361173X-RAY DIFFRACTION100
4.6597-5.01840.33191410.28281214X-RAY DIFFRACTION100
5.0184-5.52150.30271250.30861263X-RAY DIFFRACTION100
5.5215-6.31590.2831310.31681240X-RAY DIFFRACTION100
6.3159-7.940.35641040.29431252X-RAY DIFFRACTION100
7.94-33.64590.31411030.2561277X-RAY DIFFRACTION99

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