8KD0

Crystal structure of SAR11_0769 from 'Candidatus Pelagibacter ubique' HTCC1062 bound to a co-purified ligand, beta-galactopyranose

• PDB DOI: https://doi.org/10.2210/pdb8KD0/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Candidatus Pelagibacter ubique HTCC1062
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-08 Released: 2024-07-17 
• Deposition Author(s): Clifton, B.E., Laurino, P.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.229 
• R-Value Work: 0.194 

Starting Model: experimental

Literature

Crystal structure of SAR11_0769 from 'Candidatus Pelagibacter ubique' HTCC1062 bound to a co-purified ligand, beta-galactopyranose

Clifton, B.E., Alcolombri, U., Jackson, C.J., Laurino, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.11 kDa 
• Atom Count: 3,045 
• Modelled Residue Count: 397 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable binding protein component of ABC sugar transporter	A	418	Candidatus Pelagibacter ubique HTCC1062	Mutation(s): 0  Gene Names: SAR11_0769
UniProt
Find proteins for Q4FMK2 (Pelagibacter ubique (strain HTCC1062)) Explore Q4FMK2  Go to UniProtKB:  Q4FMK2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAL (Subject of Investigation/LOI)	B [auth A]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.229 
• R-Value Work: 0.194 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.879	α = 90
b = 43.879	β = 90
c = 328.555	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Clifton, B.E., Laurino, P.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release