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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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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

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

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.