8YAV | pdb_00008yav

Crystal structure of glucose 1-dehydrogenase from Limosilactobacillus fermentum

PDB DOI: https://doi.org/10.2210/pdb8YAV/pdb

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

Deposited: 2024-02-10 Released: 2024-10-30
Deposition Author(s): Cong, L., Wang, J.J., Wei, H.L., Liu, W.D., You, S.
Funding Organization(s): Chinese Scholarship Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.217 (Depositor), 0.219 (DCC)
R-Value Work:
0.189 (Depositor), 0.192 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure-Guided Engineering of a Short-Chain Dehydrogenase LfSDR1 for Efficient Biosynthesis of (R)-9-(2-Hydroxypropyl)adenine, the Key Intermediate of Tenofovir.

Wang, Q., Cong, L., Guo, J., Wang, J., Han, X., Zhang, W., Liu, W., Wei, H., You, S.

(2024) Adv Synth Catal n/a

DOI: https://doi.org/10.1002/adsc.202400752

Macromolecule Content

Total Structure Weight: 105.34 kDa
Atom Count: 7,916
Modeled Residue Count: 984
Deposited Residue Count: 988
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SDR family oxidoreductase	A, B, C, D	247	Limosilactobacillus fermentum	Mutation(s): 1 Gene Names: GC247_10055 EC: 1.1.1.163 (UniProt), 1.1.1.53 (UniProt), 1.1.1.51 (UniProt), 1.1.1.47 (UniProt)
UniProt
Find proteins for A0A1D7ZZ64 (Limosilactobacillus fermentum) Explore A0A1D7ZZ64 Go to UniProtKB: A0A1D7ZZ64
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1D7ZZ64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.217 (Depositor), 0.219 (DCC)
R-Value Work: 0.189 (Depositor), 0.192 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.851	α = 70.58
b = 58.079	β = 83.46
c = 73.072	γ = 78.36

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Scholarship Council	China	--

Revision History (Full details and data files)

Version 1.0: 2024-10-30
Type: Initial release
Version 1.1: 2026-03-04
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.