7BAY | pdb_00007bay

Crystal structure of CbpF from Streptococcus pneumoniae complexed with a Ytterbium derivative

• PDB DOI: https://doi.org/10.2210/pdb7BAY/pdb

• Classification: CHOLINE-BINDING PROTEIN
• Organism(s): Streptococcus pneumoniae R6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-12-16 Released: 2021-07-21 
• Deposition Author(s): Martinez Caballero, S., Hermoso, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.242 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

First Lanthanide Complex for De Novo Phasing in Native Protein Crystallography at 1 angstrom Radiation

Prieto-Castaneda, A., Martinez-Caballero, S., Agarrabeitia, A.R., Garcia-Moreno, I., Moya, S.D.L., Ortiz, M.J., Hermoso, J.A.

(2021) ACS Appl Bio Mater 4: 4575-4581

• DOI: https://doi.org/10.1021/acsabm.1c00305

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 38 kDa 
• Atom Count: 2,727 
• Modeled Residue Count: 311 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline-binding protein F	A [auth AA]	311	Streptococcus pneumoniae R6	Mutation(s): 0  Gene Names: cbpF, spr0337
UniProt
Find proteins for Q8DR52 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DR52  Go to UniProtKB:  Q8DR52

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T7K	L [auth AA]	neutral Yb(III)-caged complex C21 H29 N4 O7 Yb CKUMJXQWUQKKED-UHFFFAOYSA-K
PGE	E [auth AA]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CHT	B [auth AA], C [auth AA], D [auth AA], F [auth AA], G [auth AA], I [auth AA]	CHOLINE ION C5 H14 N O OEYIOHPDSNJKLS-UHFFFAOYSA-N
GOL	H [auth AA], J [auth AA], K [auth AA]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.242 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.904	α = 90
b = 52.207	β = 90
c = 73.99	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Martinez Caballero, S., Hermoso, J.A.

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description