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- PDB-5e9s: Crystal structure of substrate-bound glutamate transporter homolo... -

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Basic information

Entry
Database: PDB / ID: 5e9s
TitleCrystal structure of substrate-bound glutamate transporter homologue GltTk
ComponentsProton/glutamate symporter, SDF family
KeywordsTRANSPORT PROTEIN / AMINO ACID TRANSPORTER / ASPARTATE TRANSPORT / GLUTAMATE TRANSPORT 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
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
AuthorsGuskov, A. / Slotboom, D.J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
NWO865.11.001 Netherlands
CitationJournal: Nat Commun / Year: 2016
Title: Coupled binding mechanism of three sodium ions and aspartate in the glutamate transporter homologue GltTk.
Authors: Guskov, A. / Jensen, S. / Faustino, I. / Marrink, S.J. / Slotboom, D.J.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Jan 10, 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)149,74370
Polymers140,0563
Non-polymers9,68767
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26920 Å2
ΔGint-13 kcal/mol
Surface area50630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.520, 117.520, 310.590
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, 6 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 (archaea) / Gene: TK0986 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JID0
#4: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 6 types, 64 molecules

#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: Na
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.52 Å3/Da / Density % sol: 72.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 400, 3% Xylitol, 50mM MgCl2, 150mM NaCl, 100mM Glycine pH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48.4 Å / Num. obs: 60568 / % possible obs: 97.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.3
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.3 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KY0

4ky0


Resolution: 2.8→48.358 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 2009 3.32 %Random selection
Rwork0.2126 ---
obs0.2136 60568 97.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→48.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9554 0 643 0 10197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810333
X-RAY DIFFRACTIONf_angle_d1.13113843
X-RAY DIFFRACTIONf_dihedral_angle_d13.776042
X-RAY DIFFRACTIONf_chiral_restr0.0611684
X-RAY DIFFRACTIONf_plane_restr0.0081637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.41791370.40044048X-RAY DIFFRACTION96
2.9476-3.03430.35421390.35294125X-RAY DIFFRACTION98
3.5276-3.71350.25111460.20144168X-RAY DIFFRACTION98
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)
11.75450.3449-0.6051.54990.40233.053-0.0882-0.21340.13070.1603-0.0967-0.1258-0.72120.43060.12290.847-0.2106-0.21970.5616-0.0220.6269-18.11881.8804127.6407
23.2922-0.45641.2621.8411-0.68013.17430.0195-0.45390.04870.4242-0.15750.16370.1317-0.99110.19550.7031-0.25030.10340.9003-0.08780.4826-52.661355.2865135.8174
31.3932-0.26070.2481.98970.65013.33870.0244-0.119-0.30750.8061-0.0246-0.35540.90470.5261-0.00730.89180.0328-0.21220.64160.16480.7699-12.05738.0657130.6621
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 5 through 500)
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 500)
3X-RAY DIFFRACTION3(chain 'C' and resid 5 through 500)

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