[English] 日本語
Yorodumi
- PDB-6r7r: Crystal structure of the glutamate transporter homologue GltTk in... -

+
Open data


ID or keywords:

Loading...

-
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


dicarboxylic 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
Components

-
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

-
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


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


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


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


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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more