9G4C | pdb_00009g4c

25-phosphosteroid lyase + phosphate + desmost-1,4-diene-3-one

PDB DOI: https://doi.org/10.2210/pdb9G4C/pdb

Classification: LYASE
Organism(s): Sterolibacterium denitrificans
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-07-15 Released: 2026-01-28
Deposition Author(s): Ermler, U., Boll, M., Demmer, U., Jacoby, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.290 (Depositor), 0.290 (DCC)
R-Value Work:
0.237 (Depositor), 0.239 (DCC)
R-Value Observed:
0.240 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Structure and mechanism of the 25-phosphosteroid lyase

C Jacoby, C., Demmer, U., Ermler, U., Boll, M.

To be published.

Macromolecule Content

Total Structure Weight: 167.38 kDa
Atom Count: 11,841
Modeled Residue Count: 1,442
Deposited Residue Count: 1,448
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
25-phosphosteroid lyase	A, B, C, D	362	Sterolibacterium denitrificans	Mutation(s): 0 Gene Names: SDENCHOL_21320
UniProt
Find proteins for A0A7Z7MWD0 (Sterolibacterium denitrificans) Explore A0A7Z7MWD0 Go to UniProtKB: A0A7Z7MWD0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7Z7MWD0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IIL (Subject of Investigation/LOI) Query on A1IIL Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain F [auth B] MOL2 format, chain M [auth D] MOL2 format, chain F [auth B] mmCIF format, chain M [auth D] mmCIF format, chain F [auth B]	F [auth B], M [auth D]	(8~{R},9~{S},10~{R},13~{R},14~{R},17~{S})-10,13-dimethyl-17-[(2~{R})-6-methylhept-5-en-2-yl]-6,7,8,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthren-3-one C₂₇ H₄₀ O QZDFWWJJVPACDE-DZYNJOPRSA-N		Interactions Focus chain F [auth B] Focus chain M [auth D] Interactions & Density Focus chain F [auth B] Focus chain M [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], J [auth C], N [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain N [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B]	H [auth B], K [auth C], L [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain I [auth B] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain I [auth B] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain I [auth B]	I [auth B], O [auth D], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain I [auth B] Focus chain O [auth D] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.290 (Depositor), 0.290 (DCC)
R-Value Work: 0.237 (Depositor), 0.239 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.26	α = 90
b = 155.48	β = 90
c = 96.72	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	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: 2026-01-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-01-28
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.