8ZAX

Crystal structure of a short-chain dehydrogenase from Lactobacillus fermentum with NADPH

PDB DOI: https://doi.org/10.2210/pdb8ZAX/pdb

Classification: HYDROLASE
Organism(s): Limosilactobacillus fermentum
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2024-04-25 Released: 2024-10-30
Deposition Author(s): Wang, J.J., Cong, L., Wei, H.L., Liu, W.D., You, S.
Funding Organization(s): Chinese Scholarship Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.248 (Depositor), 0.263 (DCC)
R-Value Work:
0.217 (Depositor), 0.232 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 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

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

Macromolecule Content

Total Structure Weight: 54.13 kDa
Atom Count: 4,201
Modelled Residue Count: 492
Deposited Residue Count: 494
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SDR family oxidoreductase	A, B	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1D7ZZ64
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.248 (Depositor), 0.263 (DCC)
R-Value Work: 0.217 (Depositor), 0.232 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.827	α = 90
b = 88.818	β = 90
c = 157.371	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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

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.