5LFC | pdb_00005lfc

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

PDB DOI: https://doi.org/10.2210/pdb5LFC/pdb

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

Deposited: 2016-07-01 Released: 2017-10-11
Deposition Author(s): Claverie, M., Cioci, G., Remaud-simeon, M., Moulis, C., Tranier, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.248 (Depositor), 0.248 (DCC)
R-Value Work:
0.221 (Depositor), 0.222 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5LFC

This is version 1.1 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: 288.8 kDa
Atom Count: 18,029
Modeled Residue Count: 2,296
Deposited Residue Count: 2,586
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DsrV	A, B	1,293	Leuconostoc citreum	Mutation(s): 0 Gene Names: dsrV EC: 2.4.1.5
UniProt
Find proteins for A0A2H4A2M1 (Leuconostoc citreum) Explore A0A2H4A2M1 Go to UniProtKB: A0A2H4A2M1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2H4A2M1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.248 (Depositor), 0.248 (DCC)
R-Value Work: 0.221 (Depositor), 0.222 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.84	α = 90
b = 128.71	β = 90
c = 229.34	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-10-11

Deposition Author(s):

Remaud-simeon, M.

Revision History (Full details and data files)

Version 1.0: 2017-10-11
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.