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- PDB-6zgb: glutamate transporter homologue Glttk in complex with a photo cag... -

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Basic information

Entry
Database: PDB / ID: 6zgb
Titleglutamate transporter homologue Glttk in complex with a photo cage compound
ComponentsProton/glutamate symporter, SDF family
KeywordsTRANSPORT PROTEIN / glutamate transporter / photo cage / membrane protein
Function / homology
Function and homology information


dicarboxylic acid transport / symporter activity / membrane / plasma membrane
Similarity search - Function
Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-QJW / Proton/glutamate symporter, SDF family
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsArkhipova, V. / Slotboom, D.J. / Guskov, A.
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 18, 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 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 / 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

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)141,48311
Polymers140,0563
Non-polymers1,4278
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-59 kcal/mol
Surface area49330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.740, 115.740, 308.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
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
11ARGARGLEULEU(chain A and (resid 8 through 186 or resid 188 through 430))AA8 - 1868 - 186
12VALVALSERSER(chain A and (resid 8 through 186 or resid 188 through 430))AA188 - 430188 - 430
21ARGARGLEULEU(chain B and (resid 8 through 186 or resid 188 through 430))BB8 - 1868 - 186
22VALVALSERSER(chain B and (resid 8 through 186 or resid 188 through 430))BB188 - 430188 - 430
31ARGARGLEULEU(chain C and (resid 8 through 186 or resid 188 through 430))CC8 - 1868 - 186
32VALVALSERSER(chain C and (resid 8 through 186 or resid 188 through 430))CC188 - 430188 - 430

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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
Details: 8 His tag at C-terminus
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-QJW / (2~{S},3~{S})-2-azanyl-3-[(2-nitrophenyl)methoxy]butanedioic acid


Mass: 284.222 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12N2O7
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
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: 4.26 Å3/Da / Density % sol: 71.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 27%PEG350MME, 100 mM Tris 8.0, 40 mM NaCl

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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: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 40350 / % possible obs: 99.7 % / Redundancy: 7.58 % / CC1/2: 0.998 / Net I/σ(I): 9.16
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 7.83 % / Num. unique obs: 2923 / CC1/2: 0.145 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DWY

5dwy


Resolution: 3.2→45.748 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.04
RfactorNum. reflection% reflection
Rfree0.2745 2017 5.01 %
Rwork0.2319 --
obs0.234 40289 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 356.89 Å2 / Biso mean: 153.2887 Å2 / Biso min: 72.05 Å2
Refinement stepCycle: final / Resolution: 3.2→45.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9474 0 98 0 9572
Biso mean--193.13 --
Num. residues----1271
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5643X-RAY DIFFRACTION16.033TORSIONAL
12B5643X-RAY DIFFRACTION16.033TORSIONAL
13C5643X-RAY DIFFRACTION16.033TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2-3.27990.48231410.43072677100
3.2799-3.36860.44941420.40532698100
3.3686-3.46770.45091430.37462710100
3.4677-3.57960.3751420.30992697100
3.5796-3.70750.31420.27682714100
3.7075-3.85580.30531440.24312719100
3.8558-4.03120.26961410.23482692100
4.0312-4.24360.29741430.21512726100
4.2436-4.50930.2441430.18222711100
4.5093-4.85710.23281450.1803273699
4.8571-5.34520.24381440.1887272899
5.3452-6.11710.27331470.22752782100
6.1171-7.70090.25741480.23722808100
7.7009-450.25381520.2255287498
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)
12.1247-1.2446-0.27851.70930.81914.4274-0.23540.2393-0.1527-0.4957-0.03250.1157-0.7752-0.34750.21081.4441-0.0573-0.00420.86190.05370.752442.52917.078918.5584
22.14290.96120.93183.77050.50221.5119-0.69220.4261-0.0025-0.70620.6694-0.4318-0.4570.6669-0.02420.9254-0.09140.19921.1997-0.18880.825877.2151-9.758624.7053
32.0751-1.2331.10692.47010.80955.4017-0.08260.1016-0.0664-0.3107-0.5549-0.04040.5471-0.55650.54281.2819-0.39280.19251.2528-0.17330.833736.0445-25.494228.1164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 431)A7 - 431
2X-RAY DIFFRACTION2(chain 'B' and resid 8 through 430)B8 - 430
3X-RAY DIFFRACTION3(chain 'C' and resid 8 through 430)C8 - 430

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