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- PDB-4dji: Structure of glutamate-GABA antiporter GadC -

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Basic information

Entry
Database: PDB / ID: 4dji
TitleStructure of glutamate-GABA antiporter GadC
ComponentsProbable glutamate/gamma-aminobutyrate antiporter
KeywordsTRANSPORT PROTEIN / LeuT fold / glutamate-GABA antiporter
Function / homologyGlutamate:g-aminobutyrate antiporter / Amino acid/polyamine transporter I / Amino acid permease / intracellular pH elevation / amino acid transport / antiporter activity / plasma membrane / Glutamate/gamma-aminobutyrate antiporter
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.187 Å
AuthorsMa, D. / Lu, P.L. / Yan, C.Y. / Fan, C. / Yin, P. / Wang, J.W. / Shi, Y.G.
CitationJournal: Nature / Year: 2012
Title: Structure and mechanism of a glutamate-GABA antiporter
Authors: Ma, D. / Lu, P.L. / Yan, C.Y. / Fan, C. / Yin, P. / Wang, J.W. / Shi, Y.G.
History
DepositionFeb 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Mar 20, 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: Probable glutamate/gamma-aminobutyrate antiporter
B: Probable glutamate/gamma-aminobutyrate antiporter


Theoretical massNumber of molelcules
Total (without water)110,2282
Polymers110,2282
Non-polymers00
Water0
1
A: Probable glutamate/gamma-aminobutyrate antiporter


Theoretical massNumber of molelcules
Total (without water)55,1141
Polymers55,1141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable glutamate/gamma-aminobutyrate antiporter


Theoretical massNumber of molelcules
Total (without water)55,1141
Polymers55,1141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-16 kcal/mol
Surface area37230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.618, 105.415, 188.617
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 Probable glutamate/gamma-aminobutyrate antiporter / GadC / Extreme acid sensitivity protein


Mass: 55114.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: gadC / Production host: Escherichia coli (E. coli) / References: UniProt: P63235

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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: 3.5 Å3/Da / Density % sol: 64.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% PEG400, 100mM Tris-HCl, 200mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 11, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.187→40 Å / Num. all: 26653 / Num. obs: 22522 / % possible obs: 84.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 89.21 Å2
Reflection shellResolution: 3.187→3.31 Å / % possible all: 47

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.187→35.518 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6955 / SU ML: 0.99 / σ(F): 1.35 / Phase error: 35.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3277 1146 5.13 %
Rwork0.3096 21209 -
obs0.3106 22355 84.24 %
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.768 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso max: 257.79 Å2 / Biso mean: 108.5685 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--19.8108 Å2-0 Å2-0 Å2
2---3.9388 Å20 Å2
3----4.8407 Å2
Refinement stepCycle: LAST / Resolution: 3.187→35.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7342 0 0 0 7342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157527
X-RAY DIFFRACTIONf_angle_d1.6410276
X-RAY DIFFRACTIONf_chiral_restr0.1021257
X-RAY DIFFRACTIONf_plane_restr0.0181245
X-RAY DIFFRACTIONf_dihedral_angle_d23.6272563
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1871-3.3320.4199500.40751036108634
3.332-3.50760.39211070.37551858196560
3.5076-3.72710.3951290.38122549267882
3.7271-4.01450.37091600.36443096325699
4.0145-4.41780.32621580.312431413299100
4.4178-5.05550.30481640.266131583322100
5.0555-6.36350.40311900.337731453335100
6.3635-35.51990.25761880.26463226341497
Refinement TLS params.Method: refined / Origin x: -29.5593 Å / Origin y: -4.2023 Å / Origin z: 22.0175 Å
111213212223313233
T0.3221 Å20.1093 Å2-0.0556 Å2--0.0452 Å20.0661 Å2--0.2995 Å2
L1.2984 °20.2871 °2-0.0397 °2-1.6562 °20.433 °2--7.6525 °2
S-0.0635 Å °0.1598 Å °-0.0147 Å °-0.2188 Å °0.0484 Å °0.1916 Å °-0.8863 Å °-0.264 Å °-0.0126 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 509
2X-RAY DIFFRACTION1allB12 - 504

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