3WAD | pdb_00003wad

Crystal structure of glycosyltransferase VinC involved in the biosynthesis of vicenistatin

PDB DOI: https://doi.org/10.2210/pdb3WAD/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces halstedii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-05-02 Released: 2014-06-04
Deposition Author(s): Nango, E., Minami, A., Kumasaka, T., Eguchi, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.253 (Depositor), 0.251 (DCC)
R-Value Work:
0.202 (Depositor), 0.203 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3WAD

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

Literature

Crystal Structure of Glycosyltransferase Vinc Involved in the Biosynthesis of Vicenistatin

Nango, E., Minami, A., Kumasaka, T., Eguchi, T.

To be published.

Macromolecule Content

Total Structure Weight: 92.25 kDa
Atom Count: 6,639
Modeled Residue Count: 799
Deposited Residue Count: 838
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A, B	419	Streptomyces halstedii	Mutation(s): 0 Gene Names: vinC
UniProt
Find proteins for Q76KZ6 (Streptomyces halstedii) Explore Q76KZ6 Go to UniProtKB: Q76KZ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q76KZ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.253 (Depositor), 0.251 (DCC)
R-Value Work: 0.202 (Depositor), 0.203 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.205	α = 90
b = 130.392	β = 90
c = 140.107	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-06-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-06-04
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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.