9K8R | pdb_00009k8r

Structure of Promiscuous short chain dehydrogenase Spm14 in complex with NADPH

PDB DOI: https://doi.org/10.2210/pdb9K8R/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Spiromastix sp. SCSIO F190
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-10-24 Released: 2025-02-12
Deposition Author(s): Jing, L.Q., Peng, M., Chen, Y.Y., Ju, J.H., Wu, D.L.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.201 (Depositor), 0.203 (DCC)
R-Value Work:
0.184 (Depositor), 0.185 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Enzymatic Insights into the Unusual Formation of Benzolactone and Benzopyran in the Biosynthesis of Spiromarmycin

Chen, Y., Jing, L., Peng, M., Cai, C., Shi, J., Ge, W., Liu, Y., Shang, Z., Ma, J., Wu, D., Ju, J.

(2025) ACS Catal 15: 2809-2821

DOI: https://doi.org/10.1021/acscatal.4c07664

Macromolecule Content

Total Structure Weight: 63.49 kDa
Atom Count: 4,385
Modeled Residue Count: 575
Deposited Residue Count: 586
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spm14	A, B	293	Spiromastix sp. SCSIO F190	Mutation(s): 0 EC: 1
UniProt
Find proteins for A0A8J9S3B0 (Diaporthe leptostromiformis) Explore A0A8J9S3B0 Go to UniProtKB: A0A8J9S3B0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8J9S3B0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.201 (Depositor), 0.203 (DCC)
R-Value Work: 0.184 (Depositor), 0.185 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.285	α = 90
b = 123.285	β = 90
c = 98.611	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-02-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2025-02-12
Type: Initial release
Version 1.1: 2025-09-03
Changes: Database references

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.