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- PDB-4atv: STRUCTURE OF A TRIPLE MUTANT OF THE NHAA DIMER, CRYSTALLISED AT LOW PH -

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Basic information

Entry
Database: PDB / ID: 4atv
TitleSTRUCTURE OF A TRIPLE MUTANT OF THE NHAA DIMER, CRYSTALLISED AT LOW PH
ComponentsNA(+)/H(+) ANTIPORTER NHAA
KeywordsMEMBRANE PROTEIN / TRANSPORTER / SODIUM PROTON 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 / MOLECULAR REPLACEMENT / Resolution: 3.5 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 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: 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 1.3May 1, 2024Group: 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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)174,8829
Polymers173,9884
Non-polymers8955
Water00
1
A: NA(+)/H(+) ANTIPORTER NHAA
B: NA(+)/H(+) ANTIPORTER NHAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6975
Polymers86,9942
Non-polymers7033
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-52.9 kcal/mol
Surface area33990 Å2
MethodPISA
2
C: NA(+)/H(+) ANTIPORTER NHAA
D: NA(+)/H(+) ANTIPORTER NHAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1864
Polymers86,9942
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-46.6 kcal/mol
Surface area34280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.760, 99.400, 140.230
Angle α, β, γ (deg.)90.00, 97.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 10:383 )
211CHAIN C AND (RESSEQ 10:383 )
112CHAIN B AND (RESSEQ 10:383 )
212CHAIN D AND (RESSEQ 10:383 )

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.299, 0.087, -0.95), (0.086, -0.989, -0.117), (-0.951, -0.117, 0.288)69.34299, 6.84418, 51.63559
2given(-0.28, 0.782, 0.557), (0.77, -0.163, 0.616), (0.573, 0.602, -0.557)4.09806, -27.26836, 32.98709
3given(-0.387, -0.864, 0.321), (-0.809, 0.152, -0.568), (0.443, -0.479, -0.758)19.51491, 56.59236, 46.4568

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Components

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


Mass: 43496.887 Da / Num. of mol.: 4 / Mutation: YES
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 / Variant (production host): C43 / References: UniProt: P13738
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: 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
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 109 TO THR ENGINEERED RESIDUE IN CHAIN A, GLN 277 TO GLY ...ENGINEERED RESIDUE IN CHAIN A, ALA 109 TO THR ENGINEERED RESIDUE IN CHAIN A, GLN 277 TO GLY ENGINEERED RESIDUE IN CHAIN A, LEU 296 TO MET ENGINEERED RESIDUE IN CHAIN B, ALA 109 TO THR ENGINEERED RESIDUE IN CHAIN B, GLN 277 TO GLY ENGINEERED RESIDUE IN CHAIN B, LEU 296 TO MET ENGINEERED RESIDUE IN CHAIN C, ALA 109 TO THR ENGINEERED RESIDUE IN CHAIN C, GLN 277 TO GLY ENGINEERED RESIDUE IN CHAIN C, LEU 296 TO MET ENGINEERED RESIDUE IN CHAIN D, ALA 109 TO THR ENGINEERED RESIDUE IN CHAIN D, GLN 277 TO GLY ENGINEERED RESIDUE IN CHAIN D, LEU 296 TO MET

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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 LIS04 AND 26% PEG 400 WITH 1% FACADE-EM AND 1% HEPTYL-THIOL-B-D-GLUCOSIDE AS ADDITIVES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2011
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.5→56 Å / Num. obs: 37951 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 157.22 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 22
Reflection shellResolution: 3.5→3.54 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.4 / % possible all: 69.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PRELIMINARY MODEL

Resolution: 3.5→56.98 Å / SU ML: 0.51 / σ(F): 1.31 / Phase error: 40.03 / Stereochemistry target values: ML
Details: REBUILDING WAS CARRIED OUT WITH AVERAGED MAPS. SULPHATE AND DDM WERE TENTATIVELY MODELLED INTO DENSITY AT THE DIMER INTERFACE BUT THE DENSITY COULD EQUALLY WELL ARISE FROM BOUND LIPIDS ETC.
RfactorNum. reflection% reflection
Rfree0.3127 4053 5.5 %
Rwork0.2866 --
obs0.288 73588 94.15 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.592 Å2 / ksol: 0.22 e/Å3
Displacement parametersBiso mean: 214 Å2
Baniso -1Baniso -2Baniso -3
1--4.7908 Å20 Å255.1858 Å2
2--4.6336 Å20 Å2
3---0.1571 Å2
Refinement stepCycle: LAST / Resolution: 3.5→56.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11282 0 49 0 11331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411568
X-RAY DIFFRACTIONf_angle_d0.94115775
X-RAY DIFFRACTIONf_dihedral_angle_d13.8223989
X-RAY DIFFRACTIONf_chiral_restr0.0661960
X-RAY DIFFRACTIONf_plane_restr0.0041902
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2791X-RAY DIFFRACTIONPOSITIONAL
12C2791X-RAY DIFFRACTIONPOSITIONAL0.009
21B2791X-RAY DIFFRACTIONPOSITIONAL
22D2791X-RAY DIFFRACTIONPOSITIONAL0.018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.54120.36631030.4341664X-RAY DIFFRACTION65
3.5412-3.58440.42821110.41461748X-RAY DIFFRACTION69
3.5844-3.62970.3589810.38811801X-RAY DIFFRACTION70
3.6297-3.67750.4206760.38261776X-RAY DIFFRACTION70
3.6775-3.72780.378330.38192256X-RAY DIFFRACTION83
3.7278-3.7811000.38832632X-RAY DIFFRACTION99
3.7811-3.83750.36474130.3692228X-RAY DIFFRACTION98
3.8375-3.89750.305670.37992653X-RAY DIFFRACTION98
3.8975-3.96130.36341640.3592461X-RAY DIFFRACTION98
3.9613-4.02960.41211690.35252496X-RAY DIFFRACTION99
4.0296-4.10290.405120.33172679X-RAY DIFFRACTION99
4.1029-4.18180.38623540.3432301X-RAY DIFFRACTION99
4.1818-4.26710.260340.3252690X-RAY DIFFRACTION99
4.2671-4.35990.34153250.30982309X-RAY DIFFRACTION99
4.3599-4.4612000.28222675X-RAY DIFFRACTION99
4.4612-4.57280.2842770.25452378X-RAY DIFFRACTION99
4.5728-4.69630.055420.23892674X-RAY DIFFRACTION99
4.6963-4.83450.25672720.25092361X-RAY DIFFRACTION99
4.8345-4.99040.36391230.26482572X-RAY DIFFRACTION99
4.9904-5.16870.29161100.27512551X-RAY DIFFRACTION99
5.1687-5.37550.35912000.29782476X-RAY DIFFRACTION99
5.3755-5.61990.33741920.29682484X-RAY DIFFRACTION100
5.6199-5.91590.3363940.29662596X-RAY DIFFRACTION100
5.9159-6.28610.30071180.28642548X-RAY DIFFRACTION100
6.2861-6.77080.31522140.28572480X-RAY DIFFRACTION99
6.7708-7.45080.26321270.24642572X-RAY DIFFRACTION100
7.4508-8.52590.22031590.19352522X-RAY DIFFRACTION100
8.5259-10.730.19811750.19862505X-RAY DIFFRACTION99
10.73-56.98710.41351480.35242447X-RAY DIFFRACTION96
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)
12.7354-1.75780.0723.3028-0.14921.36790.40120.19470.15760.1369-0.35610.7452-0.1008-0.72760.00011.3916-0.062-0.01561.29920.02181.460228.52621.19958.3987
23.0765-2.560.56235.9424-1.20172.5921-0.036-0.4753-0.14250.4835-0.19730.16560.35010.18750.00021.4527-0.0676-0.09811.44750.04421.194155.0806-12.209824.1058
34.8869-4.7768-0.88522.325-1.5552-0.3806-0.5347-0.457-1.55490.57850.36191.11080.52720.43260.00772.1589-0.24610.70152.172-0.08681.816617.3593-3.57657.4091
45.2027-1.10591.14646.167-1.01640.9053-0.13640.70250.02230.49530.15091.0905-0.5972-0.943-0.00041.55020.06510.53752.0796-0.34661.6582-7.112131.99343.2546
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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