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- PDB-9oqy: X-ray crystal structure of Asp/Ala exchanger AspT at outward-faci... -

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Basic information

Entry
Database: PDB / ID: 9oqy
TitleX-ray crystal structure of Asp/Ala exchanger AspT at outward-facing conformation
ComponentsAspartate/alanine antiporter
KeywordsMEMBRANE PROTEIN / exchanger / pH homeostasis / elevator mechanism
Function / homologyYidE/YbjL duplication / Aspartate-alanine antiporter / Predicted Permease Membrane Region / : / antiporter activity / identical protein binding / plasma membrane / Aspartate/alanine antiporter
Function and homology information
Biological speciesTetragenococcus halophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsNanatani, K. / Hidaka, M. / Ogasawara, S. / Murata, T. / Abe, K. / Guan, L.
Funding support United States, Japan, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM153222 United States
Japan Society for the Promotion of Science (JSPS)16K07653 Japan
Japan Society for the Promotion of Science (JSPS)17KK0148 Japan
CitationJournal: Commun Biol / Year: 2025
Title: Elucidation of the structure and molecular mechanisms of the aspartate antiporter.
Authors: Nanatani, K. / Guan, L. / Kanno, R. / Kawabata, T. / Watanabe, S. / Katsube, S. / Hariharan, P. / Hidaka, M. / Yamanaka, T. / Toda, K. / Fujiki, T. / Kunii, K. / Miyamoto, A. / Chiba, F. / ...Authors: Nanatani, K. / Guan, L. / Kanno, R. / Kawabata, T. / Watanabe, S. / Katsube, S. / Hariharan, P. / Hidaka, M. / Yamanaka, T. / Toda, K. / Fujiki, T. / Kunii, K. / Miyamoto, A. / Chiba, F. / Ogasawara, S. / Murata, T. / Inaba, K. / Mitsuoka, K. / Abe, K. / Yamamoto, M. / Koshiba, S.
History
DepositionMay 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Aspartate/alanine antiporter


Theoretical massNumber of molelcules
Total (without water)58,0841
Polymers58,0841
Non-polymers00
Water00
1
A: Aspartate/alanine antiporter

A: Aspartate/alanine antiporter


Theoretical massNumber of molelcules
Total (without water)116,1682
Polymers116,1682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)100.688, 100.688, 354.694
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Aspartate/alanine antiporter


Mass: 58084.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetragenococcus halophilus (bacteria) / Gene: aspT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q8L3K8
Has protein modificationN

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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: 3.87 Å3/Da / Density % sol: 68.21 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 35% PEG 600, 100 mM cacodylic acid (pH 6.9), 200 mM CaCl2, 50 mM TEAP, 0.015% LMNG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.45→20 Å / Num. obs: 11832 / % possible obs: 94.6 % / Redundancy: 7.4 % / Biso Wilson estimate: 116.33 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.07 / Rrim(I) all: 0.156 / Net I/σ(I): 9.2
Reflection shellResolution: 3.45→3.78 Å / Num. unique obs: 2825 / CC1/2: 0.903 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.45→19.85 Å / SU ML: 0.3808 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.8944
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.305 584 4.98 %
Rwork0.2516 11141 -
obs0.2542 11725 94.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 124.69 Å2
Refinement stepCycle: LAST / Resolution: 3.45→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 0 0 4056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224133
X-RAY DIFFRACTIONf_angle_d0.47595621
X-RAY DIFFRACTIONf_chiral_restr0.038697
X-RAY DIFFRACTIONf_plane_restr0.0037698
X-RAY DIFFRACTIONf_dihedral_angle_d11.22751429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.790.39751530.32182755X-RAY DIFFRACTION95.66
3.8-4.340.32111510.24992765X-RAY DIFFRACTION94.61
4.34-5.450.27021410.23632754X-RAY DIFFRACTION93.63
5.45-19.850.29011390.24352867X-RAY DIFFRACTION92.27
Refinement TLS params.Method: refined / Origin x: -5.44266181901 Å / Origin y: -36.7627327192 Å / Origin z: -10.9206249268 Å
111213212223313233
T1.63515327043 Å2-0.0186964707729 Å20.003742084099 Å2-1.53264604561 Å2-0.00520601017365 Å2--0.270023857755 Å2
L0.911335858508 °2-0.0515763308507 °2-0.142471457985 °2-0.631890451962 °2-0.171851826179 °2--1.70749880894 °2
S-0.130335988975 Å °0.0585671030004 Å °0.153036995128 Å °0.358452050533 Å °0.123444683961 Å °0.00461701308558 Å °-0.61313509814 Å °-0.478832322882 Å °0.0793598283342 Å °
Refinement TLS groupSelection details: all

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