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- PDB-1zcd: Crystal structure of the Na+/H+ antiporter NhaA -

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Basic information

Entry
Database: PDB / ID: 1zcd
TitleCrystal structure of the Na+/H+ antiporter NhaA
ComponentsNa(+)/H(+) antiporter 1
KeywordsMEMBRANE PROTEIN / antiporter
Function / homology
Function and homology information


response to alkaline pH / sodium:proton antiporter activity / cardiolipin binding / response to salt stress / regulation of intracellular pH / plasma membrane
Similarity search - Function
Na+/H+ antiporter like domain / Na+/H+ antiporter like fold / Na+/H+ antiporter NhaA / Na+/H+ antiporter domain superfamily / Na+/H+ antiporter 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Na(+)/H(+) antiporter NhaA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.45 Å
AuthorsHunte, C. / Screpanti, E. / Venturi, M. / Rimon, A. / Padan, E. / Michel, H.
CitationJournal: Nature / Year: 2005
Title: Structure of a Na+/H+ antiporter and insights into mechanism of action and regulation by pH.
Authors: Hunte, C. / Screpanti, E. / Venturi, M. / Rimon, A. / Padan, E. / Michel, H.
History
DepositionApr 11, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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 1
B: Na(+)/H(+) antiporter 1


Theoretical massNumber of molelcules
Total (without water)82,7772
Polymers82,7772
Non-polymers00
Water0
1
A: Na(+)/H(+) antiporter 1


Theoretical massNumber of molelcules
Total (without water)41,3881
Polymers41,3881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Na(+)/H(+) antiporter 1


Theoretical massNumber of molelcules
Total (without water)41,3881
Polymers41,3881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.868, 121.718, 123.578
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 Na(+)/H(+) antiporter 1 / Sodium/proton antiporter 1


Mass: 41388.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nhaA / Plasmid: pAXH / Production host: Escherichia coli (E. coli) / Strain (production host): RK20 / References: UniProt: P13738

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 4.95 Å3/Da / Density % sol: 75.13 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 400, MgCl2, KCl, citrate, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.9717
SYNCHROTRONESRF ID23-120.9794
SYNCHROTRONSLS X06SA30.9686
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDFeb 9, 2004
MARMOSAIC 225 mm CCD2CCDJul 10, 2004
MARRESEARCH3CCDSep 15, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.97171
20.97941
30.96861
ReflectionResolution: 3.45→20 Å / Num. all: 21922 / Num. obs: 19993 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.4 % / Net I/σ(I): 30.5
Reflection shellResolution: 3.45→3.57 Å / % possible all: 64.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
XDSdata reduction
SOLVEphasing
SHARPphasing
CNS1.1refinement
SCALEPACKdata scaling
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.45→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.316 633 -RANDOM
Rwork0.316 ---
all0.3016 21922 --
obs0.3016 19993 91.2 %-
Refinement stepCycle: LAST / Resolution: 3.45→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5616 0 0 0 5616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01028
X-RAY DIFFRACTIONc_angle_deg1.57304

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