4QSD | pdb_00004qsd

Crystal structure of atu4361 sugar transporter from Agrobacterium Fabrum C58, target efi-510558, with bound sucrose

PDB DOI: https://doi.org/10.2210/pdb4QSD/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-07-03 Released: 2014-08-06
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free:
0.151 (Depositor), 0.167 (DCC)
R-Value Work:
0.121 (Depositor), 0.138 (DCC)
R-Value Observed:
0.122 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 3.1 of the entry. See complete history.

Literature

Crystal Structure of Maltoside Transporter Atu4361 from Agrobacterium Fabrum, Target Efi-510558

Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 46.03 kDa
Atom Count: 3,582
Modeled Residue Count: 382
Deposited Residue Count: 407
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC-TYPE SUGAR TRANSPORTER	A	407	Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: ATU4361
UniProt
Find proteins for A9CGI0 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CGI0 Go to UniProtKB: A9CGI0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9CGI0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B, C, D	2		N/A	Interactions Focus chain B Focus chain C Focus chain D Interactions & Density Focus chain B Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	B, C, D	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain B Focus chain C Focus chain D Interactions & Density Focus chain B Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free: 0.151 (Depositor), 0.167 (DCC)
R-Value Work: 0.121 (Depositor), 0.138 (DCC)
R-Value Observed: 0.122 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.025	α = 90
b = 76.564	β = 90.21
c = 67.873	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-08-06

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2014-08-06
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references, Structure summary
Version 2.0: 2020-04-08
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 3.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary