8IOX

Escherichia coli OpgD mutant-D388N

PDB DOI: https://doi.org/10.2210/pdb8IOX/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-03-13 Released: 2024-03-13
Deposition Author(s): Motouchi, S., Nakajima, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.232
R-Value Work: 0.194

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Novel glycoside hydrolase family enzymes from Escherichia coli associating with osmo-regulated periplasmic glucan synthesis

Motouchi, S., Nakajima, M.

To be published.

Macromolecule Content

Total Structure Weight: 770.22 kDa
Atom Count: 51,848
Modelled Residue Count: 6,288
Deposited Residue Count: 6,708
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucans biosynthesis protein D	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	559	Escherichia coli	Mutation(s): 1 Gene Names: opgD
UniProt
Find proteins for P40120 (Escherichia coli (strain K12)) Explore P40120 Go to UniProtKB: P40120
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40120
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	M, N, O, P, Q M, N, O, P, Q, R, S, T, U, V	2		N/A	Interactions Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Interactions & Density Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V
Glycosylation Resources
GlyTouCan: G92130SN GlyCosmos: G92130SN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.232
R-Value Work: 0.194
Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 226.75	α = 90
b = 392.76	β = 90
c = 324.648	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2024-03-13
Type: Initial release

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.