3VDN | pdb_00003vdn

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 (Depositor), 0.290 (DCC)
R-Value Work:
0.241 (Depositor), 0.240 (DCC)
R-Value Observed:
0.243 (Depositor)

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
Modeled 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 (PDB Primary Data), 2.5.1.135 (UniProt)
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 mmCIF 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 (Depositor), 0.290 (DCC)
R-Value Work: 0.241 (Depositor), 0.240 (DCC)
R-Value Observed: 0.243 (Depositor)

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

View Full Validation Report

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 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.