8WCH

Crystal structure of SAR11_0655 bound to a co-purified ligand, L-pyroglutamate

• PDB DOI: https://doi.org/10.2210/pdb8WCH/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Candidatus Pelagibacter ubique HTCC1062
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-09-12 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: 1.52 Å
• R-Value Free: 0.187 
• R-Value Work: 0.150 

Starting Model: in silico

Literature

Crystal structure of SAR11_0655 bound to a co-purified ligand, L-pyroglutamate

Clifton, B.E., 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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 90.35 kDa 
• Atom Count: 6,692 
• Modelled Residue Count: 792 
• Deposited Residue Count: 834 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable Leu/Ile/Val-binding protein	A, B	417	Candidatus Pelagibacter ubique HTCC1062	Mutation(s): 0  Gene Names: braC
UniProt
Find proteins for Q4FMW4 (Pelagibacter ubique (strain HTCC1062)) Explore Q4FMW4  Go to UniProtKB:  Q4FMW4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PCA (Subject of Investigation/LOI)	C [auth A], E [auth B]	PYROGLUTAMIC ACID C5 H7 N O3 ODHCTXKNWHHXJC-VKHMYHEASA-N
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNN	A, B	L-PEPTIDE LINKING	C4 H6 N2 O2		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.187 
• R-Value Work: 0.150 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.204	α = 90
b = 122.204	β = 90
c = 125.908	γ = 90

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