7VGK

Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI

PDB DOI: https://doi.org/10.2210/pdb7VGK/pdb

Classification: ISOMERASE
Organism(s): Lacticaseibacillus rhamnosus
Expression System: Escherichia coli B
Mutation(s): No

Deposited: 2021-09-16 Released: 2022-10-19
Deposition Author(s): Iwase, H., Oiki, S., Mikami, B., Takase, R., Hashimoto, W.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.238
R-Value Work: 0.194
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structures of Lacticaseibacillus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI in complex with substrate analogs

Iwase, H., Yamamoto, Y., Yamada, A., Kawai, K., Oiki, S., Watanabe, D., Mikami, B., Takase, R., Hashimoto, W.

(2023) J Appl Glycosci (1999)

DOI: https://doi.org/10.5458/jag.jag.JAG-2023_0003

Macromolecule Content

Total Structure Weight: 182.67 kDa
Atom Count: 12,377
Modelled Residue Count: 1,539
Deposited Residue Count: 1,596
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase	A, B, C, D, E A, B, C, D, E, F	266	Lacticaseibacillus rhamnosus	Mutation(s): 0 Gene Names: kduI, kduI1, GKD16_00900, LRHP540_00845 EC: 5.3.1.17
UniProt
Find proteins for A0A249DGV6 (Lacticaseibacillus rhamnosus) Explore A0A249DGV6 Go to UniProtKB: A0A249DGV6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A249DGV6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.238
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.19	α = 90
b = 130.98	β = 90
c = 157.315	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL2Map	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-10-19

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: 2022-10-19
Type: Initial release
Version 1.1: 2023-11-15
Changes: Data collection, Database references
Version 1.2: 2023-11-29
Changes: Refinement description

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.