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- PDB-6zlh: the structure of glutamate transporter homologue GltTk in complex... -

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Basic information

Entry
Database: PDB / ID: 6zlh
Titlethe structure of glutamate transporter homologue GltTk in complex with the photo switchable compound (trans)
ComponentsProton/glutamate symporter, SDF family
KeywordsTRANSPORT PROTEIN / glutamate transporter / amino acid transporter / photoisomerization / membrane protein
Function / homology
Function and homology information


carboxylic acid transport / symporter activity / membrane / plasma 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 / Chem-QM5 / Proton/glutamate symporter, SDF family
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsArkhipova, V. / Slotboom, D.J. / Guskov, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Structural Aspects of Photopharmacology: Insight into the Binding of Photoswitchable and Photocaged Inhibitors to the Glutamate Transporter Homologue.
Authors: Arkhipova, V. / Fu, H. / Hoorens, M.W.H. / Trinco, G. / Lameijer, L.N. / Marin, E. / Feringa, B.L. / Poelarends, G.J. / Szymanski, W. / Slotboom, D.J. / Guskov, A.
History
DepositionJun 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)146,04442
Polymers140,0563
Non-polymers5,98839
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16160 Å2
ΔGint-112 kcal/mol
Surface area51150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.790, 116.790, 310.180
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND (RESID 8 THROUGH 186 OR RESID 188 THROUGH 430))
21(CHAIN B AND (RESID 8 THROUGH 186 OR RESID 188 THROUGH 430))
31(CHAIN C AND (RESID 8 THROUGH 186 OR RESID 188 THROUGH 430))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGARGARG(CHAIN A AND (RESID 8 THROUGH 186 OR RESID 188 THROUGH 430))AA88
12VALVALVALVAL(CHAIN A AND (RESID 8 THROUGH 186 OR RESID 188 THROUGH 430))AA188188
21ARGARGARGARG(CHAIN B AND (RESID 8 THROUGH 186 OR RESID 188 THROUGH 430))BB88
22VALVALVALVAL(CHAIN B AND (RESID 8 THROUGH 186 OR RESID 188 THROUGH 430))BB188188
31ARGARGARGARG(CHAIN C AND (RESID 8 THROUGH 186 OR RESID 188 THROUGH 430))CC88
32VALVALVALVAL(CHAIN C AND (RESID 8 THROUGH 186 OR RESID 188 THROUGH 430))CC188188

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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
Details: 8His-tag at C-terminus
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
#3: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 6 types, 36 molecules

#2: Chemical ChemComp-QM5 / (2~{S},3~{S})-2-azanyl-3-[[4-[2-(4-methoxyphenyl)hydrazinyl]phenyl]methoxy]butanedioic acid


Mass: 375.376 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H21N3O6
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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

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Details

Has ligand of interestN

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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: 4.36 Å3/Da / Density % sol: 71.79 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 23% PEG 400, 100 mM sodium acetate, 50 mM NaCl, 20 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.8→49.913 Å / Num. obs: 61276 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.99 / Net I/σ(I): 9.85
Reflection shellResolution: 2.8→2.87 Å / Mean I/σ(I) obs: 0.41 / Num. unique obs: 4451 / CC1/2: 0.236 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XSCALEdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E9S

5e9s


Resolution: 2.8→49.913 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 3062 5 %
Rwork0.2178 58214 -
obs0.2195 61276 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 358.93 Å2 / Biso mean: 114.2189 Å2 / Biso min: 62.65 Å2
Refinement stepCycle: final / Resolution: 2.8→49.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9463 0 402 0 9865
Biso mean--143.27 --
Num. residues----1270
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5763X-RAY DIFFRACTIONPOSITIONAL0
12B5763X-RAY DIFFRACTIONPOSITIONAL0
13C5763X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8001-2.84390.44581380.43112613100
2.8439-2.89050.46141360.41442614100
2.8905-2.94030.39431380.39862607100
2.9403-2.99380.37111380.37992620100
2.9938-3.05140.37581350.36772571100
3.0514-3.11360.38741380.33892608100
3.1136-3.18130.37451370.32592612100
3.1813-3.25530.31071380.30682634100
3.2553-3.33670.3151370.28692618100
3.3367-3.42690.31561390.29412624100
3.4269-3.52770.32971380.26112618100
3.5277-3.64160.29061380.23262630100
3.6416-3.77170.24061390.20352638100
3.7717-3.92260.26591370.19532601100
3.9226-4.10110.22121380.19122642100
4.1011-4.31720.21441410.17162679100
4.3172-4.58750.18221390.15672649100
4.5875-4.94140.18621400.15172657100
4.9414-5.43810.2471410.16682675100
5.4381-6.22380.24661430.20472706100
6.2238-7.83640.21731440.20962739100
7.8364-49.9130.24211500.2228285999
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)
11.8741-0.07410.70382.4668-0.22852.3554-0.0640.1150.0329-0.2607-0.11390.10530.805-0.60240.16561.22-0.3042-0.01241.0645-0.11030.5687-46.300523.076228.3439
22.16170.6179-0.58191.3389-0.10733.1467-0.17720.28610.1008-0.4458-0.02710.0562-0.5975-0.11880.19541.12120.128-0.15640.7970.0880.5265-40.211366.539123.2597
32.66040.79951.13061.64950.24161.7429-0.0130.0172-0.0564-0.2919-0.0301-0.05380.31740.47940.05091.033-0.01510.1681.24710.03220.5053-5.926738.959520.211
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 8 THROUGH 501)A0
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 8 THROUGH 501)B0
3X-RAY DIFFRACTION3(CHAIN 'C' AND RESID 8 THROUGH 501)C0

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