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- PDB-4au5: Structure of the NhaA dimer, crystallised at low pH -

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Basic information

Entry
Database: PDB / ID: 4au5
TitleStructure of the NhaA dimer, crystallised at low pH
ComponentsNA(+)/H(+) ANTIPORTER NHAA
KeywordsMEMBRANE PROTEIN / TRANSPORTER
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 NhaA / Na+/H+ antiporter domain superfamily / Na+/H+ antiporter 1 / Na+/H+ antiporter like fold / 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 / MOLECULAR REPLACEMENT / Resolution: 3.696 Å
AuthorsDrew, D. / Lee, C. / Iwata, S. / Cameron, A.D.
CitationJournal: J. Gen. Physiol. / Year: 2014
Title: Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights.
Authors: Lee, C. / Yashiro, S. / Dotson, D.L. / Uzdavinys, P. / Iwata, S. / Sansom, M.S. / von Ballmoos, C. / Beckstein, O. / Drew, D. / Cameron, A.D.
History
DepositionMay 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NA(+)/H(+) ANTIPORTER NHAA
B: NA(+)/H(+) ANTIPORTER NHAA
C: NA(+)/H(+) ANTIPORTER NHAA
D: NA(+)/H(+) ANTIPORTER NHAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,7249
Polymers171,8294
Non-polymers8955
Water00
1
A: NA(+)/H(+) ANTIPORTER NHAA
B: NA(+)/H(+) ANTIPORTER NHAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6175
Polymers85,9142
Non-polymers7033
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-50.6 kcal/mol
Surface area34630 Å2
MethodPISA
2
C: NA(+)/H(+) ANTIPORTER NHAA
D: NA(+)/H(+) ANTIPORTER NHAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1064
Polymers85,9142
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-44.9 kcal/mol
Surface area34950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.800, 100.560, 141.612
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B
311CHAIN C
411CHAIN D

NCS oper:
IDCodeMatrixVector
1given(-0.289, 0.059, -0.956), (0.074, -0.994, -0.083), (-0.955, -0.094, 0.282)69.1514, 6.53442, 51.99979
2given(-0.257, 0.788, 0.559), (0.777, -0.176, 0.605), (0.575, 0.59, -0.567)3.16627, -27.07852, 33.62885
3given(-0.417, -0.855, 0.309), (-0.791, 0.174, -0.586), (0.448, -0.489, -0.749)20.81782, 56.62976, 46.45092

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Components

#1: Protein
NA(+)/H(+) ANTIPORTER NHAA / SODIUM/PROTON ANTIPORTER NHAA / SODIUM PROTON ANTIPORTER NHAA


Mass: 42957.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PWALDO GFPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: P13738
#2: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 4.8 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 3.8
Details: 0.1 M SODIUM CITRATE PH 3.8, 0.1 M LITHIUM SULPHATE, 26% PEG 400 WITH 1% HEPTYL-THIOL-B-D-GLUCOSIDE AS AN ADDITIVE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: MARRESEARCH MX300 / Detector: CCD / Date: Apr 24, 2009
RadiationMonochromator: SI(III) DOUBLE CRYSTAL MONOCHOMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.7→30 Å / Num. obs: 34273 / % possible obs: 98.1 % / Observed criterion σ(I): -1 / Redundancy: 3.4 % / Biso Wilson estimate: 133.33 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.7
Reflection shellResolution: 3.7→3.8 Å / Redundancy: 3 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.2 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZCD -FINAL REFINEMENT DONE AGAINST 4ATV

1zcd

4atv


Resolution: 3.696→29.644 Å / SU ML: 0.6 / σ(F): 1.38 / Phase error: 43.16 / Stereochemistry target values: ML
Details: RESTRAINED TO 4ATV USED SECONDARY STRUCTURE AND NCS RESTRAINTS. REFINED WITH NCS RESTRAINTS AND RESTRAINED TO 4ATV. SULPHATE AND DETERGENT TENTATIVELY MODELLED IN DIMER INTERFACE AS FOR 4ATV.
RfactorNum. reflection% reflection
Rfree0.342 1877 5.5 %
Rwork0.3179 --
obs0.3192 34183 98.16 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.901 Å2 / ksol: 0.186 e/Å3
Displacement parametersBiso mean: 205 Å2
Baniso -1Baniso -2Baniso -3
1--7.5043 Å20 Å229.2421 Å2
2--16.218 Å20 Å2
3----8.7137 Å2
Refinement stepCycle: LAST / Resolution: 3.696→29.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11294 0 49 0 11343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111580
X-RAY DIFFRACTIONf_angle_d1.28215795
X-RAY DIFFRACTIONf_dihedral_angle_d13.6383993
X-RAY DIFFRACTIONf_chiral_restr0.0811964
X-RAY DIFFRACTIONf_plane_restr0.0091906
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2794X-RAY DIFFRACTIONPOSITIONAL
12B2794X-RAY DIFFRACTIONPOSITIONAL0.105
13C2853X-RAY DIFFRACTIONPOSITIONAL0.038
14D2794X-RAY DIFFRACTIONPOSITIONAL0.083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6957-3.79540.573810.4972386X-RAY DIFFRACTION90
3.7954-3.90690.44122140.44462403X-RAY DIFFRACTION98
3.9069-4.03270.39961720.41212467X-RAY DIFFRACTION98
4.0327-4.17640.41431840.39062395X-RAY DIFFRACTION98
4.1764-4.343200.3572618X-RAY DIFFRACTION98
4.3432-4.54020.3451660.31172480X-RAY DIFFRACTION99
4.5402-4.77860.32851670.28342464X-RAY DIFFRACTION99
4.7786-5.07660.322360.28532407X-RAY DIFFRACTION98
5.0766-5.46630.35981020.30712546X-RAY DIFFRACTION99
5.4663-6.01230.40161760.32422475X-RAY DIFFRACTION99
6.0123-6.87280.34581580.32542513X-RAY DIFFRACTION99
6.8728-8.62350.26261520.23732552X-RAY DIFFRACTION100
8.6235-29.64450.3341490.30472600X-RAY DIFFRACTION99
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)
13.7224-1.9238-0.24117.9821-1.97254.81951.18970.04230.7197-0.2804-0.77620.3747-0.439-0.8298-0.0420.9613-0.13830.01020.8427-0.21460.780928.847521.40128.4344
25.2819-2.1471.19094.3585-1.25554.3444-0.3493-0.1913-0.3343-0.2264-0.0274-0.19880.9286-0.29370.37670.99870.21070.15280.65940.17860.881954.4288-12.862724.455
34.5525-4.414-0.53735.0304-1.53211.7385-0.7-1.4851-1.21660.53420.65010.66620.03140.49350.04191.6469-0.31760.69041.67150.00621.536117.3321-3.323558.0544
45.8521-1.67820.73768.6239-1.10433.1218-0.4120.908-0.63460.28740.35831.1148-0.6526-1.20290.00851.46940.19790.64061.2836-0.24561.1365-6.840332.623843.2897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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