3VDN

Crystal Structure of VldE, the pseudo-glycosyltransferase, in complex with GDP

PDB DOI: https://doi.org/10.2210/pdb3VDN/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces hygroscopicus subsp. limoneus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-01-05 Released: 2013-01-09
Deposition Author(s): Cavalier, M.C., Yim, Y.-S., Asamizu, S., Neau, D., Mahmud, T., Lee, Y.-H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.286
R-Value Work: 0.241
R-Value Observed: 0.243

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the VldE, the pseudo-glycosyltransferase, which catalyzes non-glycosidic C-N coupling in Validamycin A biosynthesis

Cavalier, M.C., Yim, Y.-S., Asamizu, S., Neau, D., Mahmud, T., Lee, Y.-H.

To be published.

Macromolecule Content

Total Structure Weight: 55.45 kDa
Atom Count: 3,796
Modelled Residue Count: 474
Deposited Residue Count: 497
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VldE	A [auth B]	497	Streptomyces hygroscopicus subsp. limoneus	Mutation(s): 0 Gene Names: vldE EC: 2.4
UniProt
Find proteins for Q15JG1 (Streptomyces hygroscopicus subsp. limoneus) Explore Q15JG1 Go to UniProtKB: Q15JG1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15JG1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B	B	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.286
R-Value Work: 0.241
R-Value Observed: 0.243
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.029	α = 90
b = 121.037	β = 90
c = 47.824	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-01-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-01-09
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.