5NGY

Crystal structure of Leuconostoc citreum NRRL B-1299 dextransucrase DSR-M

PDB DOI: https://doi.org/10.2210/pdb5NGY/pdb

Classification: TRANSFERASE
Organism(s): Leuconostoc citreum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-03-20 Released: 2017-11-01
Deposition Author(s): Claverie, M., Cioci, G., Remaud-simeon, M., Moulis, C., Tranier, S., Vuillemin, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free: 0.236
R-Value Work: 0.192
R-Value Observed: 0.195

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

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

Macromolecule Content

Total Structure Weight: 289.55 kDa
Atom Count: 18,858
Modelled Residue Count: 2,409
Deposited Residue Count: 2,580
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DSR-M glucansucrase inactive mutant E715Q	A, B	1,290	Leuconostoc citreum	Mutation(s): 0
UniProt
Find proteins for A0A2H4A2Q1 (Leuconostoc citreum) Explore A0A2H4A2Q1 Go to UniProtKB: A0A2H4A2Q1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2H4A2Q1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose	C	4		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G80662SX GlyCosmos: G80662SX GlyGen: G80662SX

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PR Query on PR Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	E [auth A] F [auth A] G [auth A] I [auth B] J [auth B] E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	PRASEODYMIUM ION Pr WCWKKSOQLQEJTE-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B]	D [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free: 0.236
R-Value Work: 0.192
R-Value Observed: 0.195
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.869	α = 90
b = 128.81	β = 90
c = 234.518	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASER	phasing
XDS	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-11-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-11-01
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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Help and Resources

5NGY

Crystal structure of Leuconostoc citreum NRRL B-1299 dextransucrase DSR-M

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)