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- PDB-5dwy: Crystal structure of a substrate-free glutamate transporter homol... -

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Basic information

Entry
Database: PDB / ID: 5dwy
TitleCrystal structure of a substrate-free glutamate transporter homologue GltTk
ComponentsProton/glutamate symporter, SDF family
KeywordsMEMBRANE PROTEIN / AMINO ACID TRANSPORTER / ASPARTATE TRANSPORT / GLUTAMATE TRANSPORT HOMOLOGUE / TRANSPORT 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Proton/glutamate symporter, SDF family
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionSep 23, 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: 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)144,73339
Polymers140,0563
Non-polymers4,67736
Water1,08160
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18110 Å2
ΔGint53 kcal/mol
Surface area50330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.010, 116.010, 308.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#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)
Gene: TK0986 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JID0
#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C4H10O3
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.28 Å3/Da / Density % sol: 71.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40% v/v Glycerol; 20% w/v PEG 4000, 1% OG, 60mM Ca2+/Mg2+, 100mM HEPES
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 52820 / % possible obs: 79 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11
Reflection shellResolution: 2.7→2.78 Å / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.49 / % possible all: 17.9

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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: 2.7→47.765 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 2634 4.99 %Random
Rwork0.1975 ---
obs0.1995 52820 78.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→47.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9559 0 311 60 9930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810107
X-RAY DIFFRACTIONf_angle_d1.12313634
X-RAY DIFFRACTIONf_dihedral_angle_d12.9795947
X-RAY DIFFRACTIONf_chiral_restr0.061668
X-RAY DIFFRACTIONf_plane_restr0.0081648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74910.4731200.4143529X-RAY DIFFRACTION16
7.197-47.77220.27311870.22563531X-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)
10.98791.01420.63991.16210.62320.4305-0.66110.71020.2515-0.5844-0.0105-0.18620.15711.4757-0.05130.99360.39980.17151.43230.27970.9153-20.939-14.995120.5038
21.224-0.27650.55391.6069-0.82371.43020.01050.0537-0.3766-0.23210.05440.08890.68770.12990.04470.9962-0.0925-0.06940.2175-0.03850.5229-48.9745-21.181121.8858
31.6484-0.45470.44151.3525-0.47751.88450.01530.3325-0.1278-0.6373-0.0137-0.01460.81340.4208-0.00210.9579-0.06780.00330.34-0.01380.4008-45.7718-13.740813.3861
41.375-0.28770.9150.54720.37781.21660.01-0.0847-0.4279-0.51230.10560.16480.5756-0.2105-0.01141.1966-0.0376-0.07110.2728-0.03070.5628-46.4938-26.340327.1673
51.430.45-0.34711.3798-0.72371.8846-0.24580.24-0.0138-0.24990.20960.43650.1447-0.89930.00810.5674-0.1536-0.16030.60240.05080.7026-79.4823.192420.9054
60.4104-0.4908-0.02420.6494-0.05930.21580.60890.51260.39630.34440.34130.2393-1.08030.8303-0.00080.8838-0.21220.19531.38-0.16560.998-82.431316.192250.3849
71.96330.2446-0.21321.1633-0.15922.3165-0.18290.32980.0262-0.29460.12530.2831-0.075-0.67550.00080.521-0.1318-0.20770.40690.05750.5308-73.424411.101318.1455
81.21960.3666-0.26241.0814-0.75470.5263-0.06240.12360.09220.29520.13210.1644-0.6573-0.59770.00020.67210.1203-0.09150.68020.07280.8297-81.726813.577934.5806
92.9148-0.3546-1.16210.45130.57010.92170.00240.66220.44790.644-0.04860.2866-1.0485-0.53290.00791.2238-0.0479-0.1270.47960.19390.8912-50.290241.876231.2074
101.69870.26780.12931.52110.70642.0318-0.1491-0.0003-0.0696-0.0254-0.1265-0.2876-0.09260.7447-0.02410.5587-0.3739-0.07880.46760.27260.4909-31.42620.319829.8247
110.98880.32610.20282.41270.10771.5681-0.16660.23410.1067-0.148-0.0615-0.0622-0.30530.3729-0.05170.6171-0.3024-0.07040.3180.1670.4045-37.78122.001220.0119
120.7201-0.2036-0.6830.9375-0.13430.861-0.1241-0.1006-0.04690.2599-0.0779-0.0159-0.0410.8343-0.00140.7092-0.3297-0.12730.64140.16860.5802-28.865923.688935.9021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 314 )
4X-RAY DIFFRACTION4chain 'A' and (resid 315 through 430 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 108 )
6X-RAY DIFFRACTION6chain 'B' and (resid 109 through 131 )
7X-RAY DIFFRACTION7chain 'B' and (resid 132 through 314 )
8X-RAY DIFFRACTION8chain 'B' and (resid 315 through 430 )
9X-RAY DIFFRACTION9chain 'C' and (resid 5 through 45 )
10X-RAY DIFFRACTION10chain 'C' and (resid 46 through 132 )
11X-RAY DIFFRACTION11chain 'C' and (resid 133 through 314 )
12X-RAY DIFFRACTION12chain 'C' and (resid 315 through 432 )

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