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- PDB-6r7r: Crystal structure of the glutamate transporter homologue GltTk in... -

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Basic information

Entry
Database: PDB / ID: 6r7r
TitleCrystal structure of the glutamate transporter homologue GltTk in complex with D-aspartate
ComponentsProton/glutamate symporter, SDF family
KeywordsTRANSPORT PROTEIN / AMINO ACID TRANSPORTER / ASPARTATE TRANSPORT / GLUTAMATE TRANSPORTER HOMOLOGUE / MEMBRANE PROTEIN
Function / homology
Function and homology information


carboxylic acid transport / symporter activity / membrane
Similarity search - Function
Proton glutamate symport protein / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
D-ASPARTIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Proton/glutamate symporter, SDF family
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsArkhipova, V. / Guskov, A. / Slotboom, D.J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research865.11.001 Netherlands
CitationJournal: Elife / Year: 2019
Title: Binding and transport of D-aspartate by the glutamate transporter homolog Glt Tk .
Authors: Arkhipova, V. / Trinco, G. / Ettema, T.W. / Jensen, S. / Slotboom, D.J. / Guskov, A.
History
DepositionMar 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.title / _citation_author.name
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proton/glutamate symporter, SDF family
B: Proton/glutamate symporter, SDF family
C: Proton/glutamate symporter, SDF family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,86635
Polymers140,0563
Non-polymers3,81032
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13560 Å2
ΔGint-72 kcal/mol
Surface area48240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.550, 116.550, 314.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Sugars , 2 types, 4 molecules ABC

#1: Protein Proton/glutamate symporter, SDF family


Mass: 46685.363 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0986 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JID0
#6: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 7 types, 31 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-DAS / D-ASPARTIC ACID / Aspartic acid


Type: D-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#9: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM

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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: 4.7 Å3/Da / Density % sol: 73.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% glycerol, 10% PEG 4000, 100 mM Tris/bicine, pH 8.0, 60 mM CaCl2, 60 mM MgCl2, 0.75% n-octyl-b-D-glucopyranoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99187 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 2.8→48.057 Å / Num. obs: 61573 / % possible obs: 99.3 % / Redundancy: 4.89 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Net I/σ(I): 8.4
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.58 % / Rmerge(I) obs: 3.768 / Num. unique obs: 4459 / CC1/2: 0.117 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E9S

5e9s


Resolution: 2.8→48.057 Å / Cross valid method: FREE R-VALUE / σ(F): 1.33
RfactorNum. reflection% reflection
Rfree0.2685 3064 4.99 %
Rwork0.2317 --
obs0.2335 61353 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9244 0 250 0 9494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089652
X-RAY DIFFRACTIONf_angle_d1.16613052
X-RAY DIFFRACTIONf_dihedral_angle_d18.2443432
X-RAY DIFFRACTIONf_chiral_restr0.061617
X-RAY DIFFRACTIONf_plane_restr0.0071579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.84380.47161370.48152610X-RAY DIFFRACTION98
2.8438-2.89040.46751280.48312443X-RAY DIFFRACTION94
2.8904-2.94030.47341380.44012626X-RAY DIFFRACTION99
2.9403-2.99370.40941400.39822676X-RAY DIFFRACTION100
2.9937-3.05130.39821370.38342606X-RAY DIFFRACTION100
3.0513-3.11360.37581370.38332605X-RAY DIFFRACTION99
3.1136-3.18130.46851380.37152640X-RAY DIFFRACTION99
3.1813-3.25530.4081390.3552637X-RAY DIFFRACTION100
3.2553-3.33660.35211390.33342643X-RAY DIFFRACTION99
3.3366-3.42680.3811400.312652X-RAY DIFFRACTION100
3.4268-3.52760.32341370.2742630X-RAY DIFFRACTION99
3.5276-3.64150.27391400.23982650X-RAY DIFFRACTION100
3.6415-3.77160.26871390.21482635X-RAY DIFFRACTION99
3.7716-3.92250.26921380.1992634X-RAY DIFFRACTION100
3.9225-4.10090.25351410.20612659X-RAY DIFFRACTION100
4.1009-4.3170.2541400.19142676X-RAY DIFFRACTION99
4.317-4.58730.22051390.17082649X-RAY DIFFRACTION99
4.5873-4.94120.21671420.16612693X-RAY DIFFRACTION100
4.9412-5.43780.23051420.18312692X-RAY DIFFRACTION100
5.4378-6.22320.2921420.21052705X-RAY DIFFRACTION99
6.2232-7.83510.22181440.21692730X-RAY DIFFRACTION98
7.8351-48.06440.24711470.23732798X-RAY DIFFRACTION96

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