9LQD | pdb_00009lqd

Crystal structure of SAM lyase

PDB DOI: https://doi.org/10.2210/pdb9LQD/pdb

Classification: IMMUNE SYSTEM
Organism(s): Clostridium botulinum A str. Hall
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-01-28 Released: 2025-11-26
Deposition Author(s): Duan, B., Zhao, B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.213 (Depositor), 0.214 (DCC)
R-Value Work:
0.197 (Depositor), 0.198 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Mechanisms of SAM-AMP synthesis and degradation in antiviral type III CRISPR signaling.

Duan, B., Zhao, B.

To be published.

Macromolecule Content

Total Structure Weight: 14.45 kDa
Atom Count: 1,037
Modeled Residue Count: 125
Deposited Residue Count: 125
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM lyase	A	125	Clostridium botulinum A str. Hall	Mutation(s): 0 Gene Names: CBO2178
UniProt
Find proteins for A5I3U9 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)) Explore A5I3U9 Go to UniProtKB: A5I3U9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5I3U9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLT (Subject of Investigation/LOI) Query on MLT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.213 (Depositor), 0.214 (DCC)
R-Value Work: 0.197 (Depositor), 0.198 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.06	α = 90
b = 118.06	β = 90
c = 118.06	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
xia2	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-11-26
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.