8HQQ

Crystal structure of the glucose-binding protein SAR11_0769 from "Candidatus Pelagibacter ubique" HTCC1062 bound to glucose

PDB DOI: https://doi.org/10.2210/pdb8HQQ/pdb

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

Deposited: 2022-12-14 Released: 2023-12-27
Deposition Author(s): Clifton, B.E., Laurino, P.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.237
R-Value Work: 0.204
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the glucose-binding protein SAR11_0769 from "Candidatus Pelagibacter ubique" HTCC1062 bound to glucose

Clifton, B.E., Laurino, P.

To be published.

Macromolecule Content

Total Structure Weight: 45.11 kDa
Atom Count: 3,071
Modelled Residue Count: 398
Deposited Residue Count: 418
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4FMK2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC (Subject of Investigation/LOI) Query on BGC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.237
R-Value Work: 0.204
R-Value Observed: 0.205
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.642	α = 90
b = 44.642	β = 90
c = 329.112	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	Japan	--

Revision History (Full details and data files)

Version 1.0: 2023-12-27
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.