5O8L | pdb_00005o8l

Crystal structure of Leuconostoc citreum NRRL B-1299 N-terminally truncated dextransucrase DSR-M in complex with sucrose

PDB DOI: https://doi.org/10.2210/pdb5O8L/pdb

Classification: TRANSFERASE
Organism(s): Leuconostoc citreum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-06-13 Released: 2017-11-29
Deposition Author(s): Claverie, M., Cioci, G., Remaud-simeon, M., Moulis, C., Tranier, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free:
0.228 (Depositor), 0.232 (DCC)
R-Value Work:
0.198 (Depositor), 0.202 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Investigations on the Determinants Responsible for Low Molar Mass Dextran Formation by DSR-M Dextransucrase

Claverie, M., Cioci, G., Vuillemin, M., Monties, N., Roblin, P., Lippens, G., Remaud-Simeon, M., Moulis, C.

(2017) ACS Catal 7: 7106-7119

DOI: https://doi.org/10.1021/acscatal.7b02182

Macromolecule Content

Total Structure Weight: 144.36 kDa
Atom Count: 8,612
Modeled Residue Count: 1,098
Deposited Residue Count: 1,290
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alternansucrase	A	1,290	Leuconostoc citreum	Mutation(s): 0 Gene Names: asr EC: 2.4.1.140 (PDB Primary Data), 2.4.1.5 (UniProt)
UniProt
Find proteins for A0A2H4A2Q1 (Leuconostoc citreum) Explore A0A2H4A2Q1 Go to UniProtKB: A0A2H4A2Q1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2H4A2Q1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.228 (Depositor), 0.232 (DCC)
R-Value Work: 0.198 (Depositor), 0.202 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.625	α = 90
b = 183.625	β = 90
c = 146.804	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-11-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-11-29
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-05-08
Changes: Data collection, Database references, Structure summary