8QB5 | pdb_00008qb5

Crystal structure of apo-GltTk obtained with in meso crystallization (P6322 space group)

• PDB DOI: https://doi.org/10.2210/pdb8QB5/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-08-24 Released: 2024-09-11 
• Deposition Author(s): Marin, E., Guskov, A., Borshchevskiy, V., Kovalev, K.
• Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.312 (Depositor), 0.307 (DCC) 
• R-Value Work: 
  0.292 (Depositor), 0.289 (DCC) 
• R-Value Observed: 
  0.293 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of apo-GltTk obtained with in meso crystallization (P6322 space group)

Marin, E., Guskov, A., Borshchevskiy, V., Kovalev, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.16 kDa 
• Atom Count: 3,069 
• Modeled Residue Count: 406 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proton/glutamate symporter, SDF family	A	430	Thermococcus kodakarensis KOD1	Mutation(s): 0  Gene Names: TK0986 Membrane Entity: Yes
UniProt
Find proteins for Q5JID0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JID0  Go to UniProtKB:  Q5JID0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	E [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA	B [auth A], C [auth A], D [auth A], F [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.312 (Depositor), 0.307 (DCC) 
• R-Value Work:  0.292 (Depositor), 0.289 (DCC) 
• R-Value Observed: 0.293 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.24	α = 90
b = 94.24	β = 90
c = 244.56	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Marin, E., Guskov, A., Borshchevskiy, V., Kovalev, K.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	OCENW.KLEIN.141

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release