4R2F | pdb_00004r2f

Crystal structure of sugar transporter ACHL_0255 from Arthrobacter chlorophenolicus A6, target EFI-510633, with bound laminaribiose

PDB DOI: https://doi.org/10.2210/pdb4R2F/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Pseudarthrobacter chlorophenolicus A6
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-08-11 Released: 2014-08-27
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: 2.00 Å
R-Value Free:
0.207 (Depositor), 0.216 (DCC)
R-Value Work:
0.165 (Depositor), 0.177 (DCC)
R-Value Observed:
0.166 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of sugar transporter ACHL_0255 from Arthrobacter chlorophenolicus, target EFI-510633

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

To be published.

Macromolecule Content

Total Structure Weight: 46.48 kDa
Atom Count: 3,300
Modeled Residue Count: 394
Deposited Residue Count: 431
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular solute-binding protein family 1	A	431	Pseudarthrobacter chlorophenolicus A6	Mutation(s): 0 Gene Names: Achl_0255
UniProt
Find proteins for B8H997 (Pseudarthrobacter chlorophenolicus (strain ATCC 700700 / DSM 12829 / CIP 107037 / JCM 12360 / KCTC 9906 / NCIMB 13794 / A6)) Explore B8H997 Go to UniProtKB: B8H997
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8H997
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G36535HU GlyCosmos: G36535HU

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900024 Query on PRD_900024	B	beta-laminaribiose	Oligosaccharide / Antimicrobial		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.207 (Depositor), 0.216 (DCC)
R-Value Work: 0.165 (Depositor), 0.177 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.101	α = 90
b = 139.101	β = 90
c = 96.458	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-08-27

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2014-08-27
Type: Initial release
Version 1.1: 2018-01-24
Changes: Advisory, Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-02-28
Changes: Advisory, Data collection, Database references, Structure summary