7BAY

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.242
R-Value Work: 0.201
R-Value Observed: 0.203

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DR52
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T7K Query on T7K Download Ideal Coordinates CCD File SDF format, chain L [auth AA] MOL2 format, chain L [auth AA]	L [auth AA]	neutral Yb(III)-caged complex C₂₁ H₂₉ N₄ O₇ Yb CKUMJXQWUQKKED-UHFFFAOYSA-K		Interactions Focus chain L [auth AA] Interactions & Density Focus chain L [auth AA]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain E [auth AA] MOL2 format, chain E [auth AA]	E [auth AA]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth AA] Interactions & Density Focus chain E [auth AA]
CHT Query on CHT Download Ideal Coordinates CCD File SDF format, chain B [auth AA] SDF format, chain C [auth AA] SDF format, chain D [auth AA] SDF format, chain F [auth AA] SDF format, chain G [auth AA] SDF format, chain I [auth AA] MOL2 format, chain B [auth AA] MOL2 format, chain C [auth AA] MOL2 format, chain D [auth AA] MOL2 format, chain F [auth AA] MOL2 format, chain G [auth AA] MOL2 format, chain I [auth AA]	B [auth AA] C [auth AA] D [auth AA] F [auth AA] G [auth AA] 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		Interactions Focus chain B [auth AA] Focus chain C [auth AA] Focus chain D [auth AA] Focus chain F [auth AA] Focus chain G [auth AA] Focus chain I [auth AA] Interactions & Density Focus chain B [auth AA] Focus chain C [auth AA] Focus chain D [auth AA] Focus chain F [auth AA] Focus chain G [auth AA] Focus chain I [auth AA]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth AA] SDF format, chain J [auth AA] SDF format, chain K [auth AA] MOL2 format, chain H [auth AA] MOL2 format, chain J [auth AA] MOL2 format, chain K [auth AA]	H [auth AA], J [auth AA], K [auth AA]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth AA] Focus chain J [auth AA] Focus chain K [auth AA] Interactions & Density Focus chain H [auth AA] Focus chain J [auth AA] Focus chain K [auth AA]