8JV3 | pdb_00008jv3

Structure of the SAR11 PotD in complex with glycine betaine

• PDB DOI: https://doi.org/10.2210/pdb8JV3/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Candidatus Pelagibacter sp. HTCC7211
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-27 Released: 2024-07-03 
• Deposition Author(s): Ma, Q., Liu, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 
  0.148 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.127 (Depositor) 

Starting Model: experimental

Literature

Structure of the SAR11 PotD in complex with glycine betaine

Ma, Q., Liu, C.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.33 kDa 
• Atom Count: 3,256 
• Modeled Residue Count: 360 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine/putrescine-binding periplasmic protein	A	361	Candidatus Pelagibacter sp. HTCC7211	Mutation(s): 0  Gene Names: potD, PB7211_697

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth A], D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PG4	E [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
BET (Subject of Investigation/LOI)	B [auth A]	TRIMETHYL GLYCINE C5 H12 N O2 KWIUHFFTVRNATP-UHFFFAOYSA-O
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free:  0.148 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.127 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.027	α = 90
b = 78.271	β = 90
c = 79.772	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Ma, Q., Liu, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	xxxx

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release