8HQR

Crystal structure of the arginine-/lysine-binding protein SAR11_1210 from 'Candidatus Pelagibacter ubique' HTCC1062 bound to arginine

PDB DOI: https://doi.org/10.2210/pdb8HQR/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Candidatus Pelagibacter ubique HTCC1062
Expression System: Escherichia coli BL21(DE3)
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: 1.32 Å
R-Value Free: 0.190
R-Value Work: 0.149
R-Value Observed: 0.151

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 arginine-/lysine-binding protein SAR11_1210 from 'Candidatus Pelagibacter ubique' HTCC1062 bound to arginine

Clifton, B.E., Laurino, P.

To be published.

Macromolecule Content

Total Structure Weight: 59.92 kDa
Atom Count: 4,603
Modelled Residue Count: 527
Deposited Residue Count: 562
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter	A, B	281	Candidatus Pelagibacter ubique HTCC1062	Mutation(s): 0 Gene Names: occT, SAR11_1210
UniProt
Find proteins for Q4FLC2 (Pelagibacter ubique (strain HTCC1062)) Explore Q4FLC2 Go to UniProtKB: Q4FLC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4FLC2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ARG (Subject of Investigation/LOI) Query on ARG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	ARGININE C₆ H₁₅ N₄ O₂ ODKSFYDXXFIFQN-BYPYZUCNSA-O		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free: 0.190
R-Value Work: 0.149
R-Value Observed: 0.151
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.128	α = 90
b = 84.689	β = 90
c = 106.097	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	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		--

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.