5BQ3

Crystal structure of a sugar ABC transporter (ACTODO_00688) from Actinomyces odontolyticus ATCC 17982 at 2.60 A resolution

PDB DOI: https://doi.org/10.2210/pdb5BQ3/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Schaalia dentiphila ATCC 17982
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-05-28 Released: 2015-08-05
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.219
R-Value Work: 0.207
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a sugar ABC transporter (ACTODO_00688) from Actinomyces odontolyticus ATCC 17982 at 2.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 139.21 kDa
Atom Count: 9,449
Modelled Residue Count: 1,250
Deposited Residue Count: 1,328
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhamnose ABC transporter, rhamnose-binding protein	A, B, C, D	332	Schaalia dentiphila ATCC 17982	Mutation(s): 0 Gene Names: rhaS, ACTODO_00688
UniProt
Find proteins for A7BAM4 (Schaalia dentiphila ATCC 17982) Explore A7BAM4 Go to UniProtKB: A7BAM4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7BAM4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.219
R-Value Work: 0.207
R-Value Observed: 0.208
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M32C70

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.78	α = 90
b = 83.28	β = 111.87
c = 104.22	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
SHELX	phasing
SHARP	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-08-05

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2015-08-05
Type: Initial release
Version 1.1: 2017-10-11
Changes: Derived calculations, Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references
Version 1.4: 2024-10-09
Changes: Data collection, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.