8ZAX | pdb_00008zax

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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Ligand Structure Quality Assessment

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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
Modeled Residue Count: 492
Deposited Residue Count: 494
Unique protein chains: 1

Macromolecules

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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% 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
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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

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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

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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.