5DU2 | pdb_00005du2

Structural analysis of EspG2 glycosyltransferase

PDB DOI: https://doi.org/10.2210/pdb5DU2/pdb

Classification: TRANSFERASE
Organism(s): Actinomadura verrucosospora
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-09-18 Released: 2015-10-14
Deposition Author(s): Michalska, K., Elshahawi, S.I., Bigelow, L., Babnigg, G., Thorson, J.S., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.236 (Depositor), 0.233 (DCC)
R-Value Work:
0.200 (Depositor), 0.201 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5DU2

This is version 1.3 of the entry. See complete history.

Literature

Structural analysis of EspG2 glycosyltransferase

Michalska, K., Elshahawi, S.I., Bigelow, L., Babnigg, G., Thorson, J.S., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

To be published.

Macromolecule Content

Total Structure Weight: 90.27 kDa
Atom Count: 5,576
Modeled Residue Count: 737
Deposited Residue Count: 838
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EspG2 glycosyltransferase	A, B	419	Actinomadura verrucosospora	Mutation(s): 0 Gene Names: espG2
UniProt
Find proteins for A0A0R4I999 (Actinomadura verrucosospora) Explore A0A0R4I999 Go to UniProtKB: A0A0R4I999
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0R4I999
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.236 (Depositor), 0.233 (DCC)
R-Value Work: 0.200 (Depositor), 0.201 (DCC)
R-Value Observed: 0.202 (Depositor)

Diffraction Data:

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.331	α = 90
b = 178.381	β = 90
c = 189.598	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MR-Rosetta	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Elshahawi, S.I.

Phillips Jr., G.N.

Midwest Center for Structural Genomics (MCSG)

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U01GM098248

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2019-12-25
Changes: Author supporting evidence
Version 1.3: 2023-09-27
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.