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

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Basic information

Entry
Database: PDB / ID: 4djk
TitleStructure of glutamate-GABA antiporter GadC
ComponentsProbable glutamate/gamma-aminobutyrate antiporter
KeywordsTRANSPORT PROTEIN / LeuT / 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: 3.097 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 area1770 Å2
ΔGint-21 kcal/mol
Surface area34210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.962, 106.408, 185.982
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: 3.23 Å3/Da / Density % sol: 61.92 %
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: SSRF / Beamline: BL17U / Wavelength: 0.97947 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 3.097→50 Å / Num. all: 31468 / Num. obs: 21370 / % possible obs: 79.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 102.05 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 26.8
Reflection shellResolution: 3.097→3.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.1 / % possible all: 19.9

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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: 3.097→33.14 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6006 / SU ML: 0.93 / σ(F): 1.34 / Phase error: 42.93 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3246 1143 5.37 %RANDOM
Rwork0.2825 20133 --
obs0.2849 21276 79.66 %-
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 91.185 Å2 / ksol: 0.247 e/Å3
Displacement parametersBiso max: 336.85 Å2 / Biso mean: 142.9525 Å2 / Biso min: 58.72 Å2
Baniso -1Baniso -2Baniso -3
1-51.3239 Å2-0 Å2-0 Å2
2---9.3413 Å20 Å2
3----41.9826 Å2
Refinement stepCycle: LAST / Resolution: 3.097→33.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6891 0 0 0 6891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017067
X-RAY DIFFRACTIONf_angle_d1.4989648
X-RAY DIFFRACTIONf_chiral_restr0.0991184
X-RAY DIFFRACTIONf_plane_restr0.0071159
X-RAY DIFFRACTIONf_dihedral_angle_d23.314190
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 (%)
3.0971-3.23790.7745340.419968171522
3.2379-3.40850.43811760.37051341151746
3.4085-3.62180.3581243174
3.6218-3.9010.4473190.33942830314995
3.901-4.29280.28423307100
4.2928-4.91230.30572690.22213051332099
4.9123-6.18240.43972120.31131613373100
6.1824-33.14230.22771330.26393331346498
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.2784-0.0153-1.24993.1673-0.86076.88190.18420.196-0.5144-1.0907-0.31960.12630.78030.34670.1580.94940.2425-0.12170.6135-0.0050.578625.257548.25139.352
21.2101-0.34060.99821.948-1.26646.77950.51240.4353-0.2298-0.1756-0.43570.03160.43090.2567-0.01410.41060.2645-0.17760.4247-0.21220.512125.591348.842742.7329
34.9289-0.61931.66515.4341.53925.0891-0.44070.51980.8038-0.79180.7422-0.37-1.75310.55940.8632-0.04270.056-0.17350.57520.00540.126624.104153.998356.0674
49.5454-3.6641-0.12774.1309-0.26933.131-0.3735-0.30370.64380.39640.2206-0.7184-0.09280.66710.13630.46420.478-0.21491.05770.00061.447621.602339.170337.9793
52.5206-0.14970.78493.037-1.06225.6041-0.3247-0.5662-0.14890.9485-0.0538-0.1888-0.9791.870.27510.77220.0465-0.25451.1977-0.04730.732631.04949.636690.7782
61.42810.52-0.27362.5273-0.0696.2818-0.27130.1030.27841.12170.1664-0.4091-1.061.1881-0.01540.77950.2338-0.15190.7734-0.21980.560130.853749.207887.3272
77.80850.6166-1.0627.97820.27415.52230.38140.6691-0.06120.9382-0.23330.4036-0.7693-0.47910.0260.59880.0946-0.02740.58010.01590.494225.999448.871273.7446
83.00361.978-0.73083.12561.73092.86280.1911.64550.84071.59411.0551-1.0423-1.0960.6565-1.47211.1711-0.2723-0.08221.3939-0.03711.727735.991758.34292.3289
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 12:180 )A12 - 180
2X-RAY DIFFRACTION2( CHAIN A AND RESID 193:403 )A193 - 403
3X-RAY DIFFRACTION3( CHAIN A AND RESID 404:466 )A404 - 466
4X-RAY DIFFRACTION4( CHAIN A AND RESID 491:501 )A491 - 501
5X-RAY DIFFRACTION5( CHAIN B AND RESID 12:181 )B12 - 181
6X-RAY DIFFRACTION6( CHAIN B AND RESID 193:403 )B193 - 403
7X-RAY DIFFRACTION7( CHAIN B AND RESID 404:468 )B404 - 468
8X-RAY DIFFRACTION8( CHAIN B AND RESID 491:501 )B491 - 501

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