7VGK | pdb_00007vgk

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 (Depositor), 0.240 (DCC)
R-Value Work:
0.194 (Depositor), 0.201 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 1,539
Deposited Residue Count: 1,596
Unique protein chains: 1

Macromolecules

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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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.194 (Depositor), 0.201 (DCC)
R-Value Observed: 0.196 (Depositor)

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

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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

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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.