9SM3 | pdb_00009sm3

gamma-PSPP-Methyltransferase from Pseudomonas chlororaphis in complex with SAH

PDB DOI: https://doi.org/10.2210/pdb9SM3/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Pseudomonas chlororaphis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-09-05 Released: 2025-12-31
Deposition Author(s): Groll, M., Yang, K., Xu, H., Troycke, P., Dickschat, J.S.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.214 (Depositor), 0.225 (DCC)
R-Value Work:
0.178 (Depositor), 0.184 (DCC)
R-Value Observed:
0.180 (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

Structural basis of methylation-triggered cyclization

Groll, M., Yang, K., Xu, H., Troycke, P., Dickschat, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 211.26 kDa
Atom Count: 14,139
Modeled Residue Count: 1,689
Deposited Residue Count: 1,830
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase domain protein	A, B, C, D, E A, B, C, D, E, F	305	Pseudomonas chlororaphis	Mutation(s): 0 Gene Names: PchlO6_6042
UniProt
Find proteins for A0AB33WUZ9 (Pseudomonas chlororaphis O6) Explore A0AB33WUZ9 Go to UniProtKB: A0AB33WUZ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AB33WUZ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain K [auth D] SDF format, chain P [auth F] SDF format, chain N [auth E] SDF format, chain J [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D] MOL2 format, chain P [auth F] MOL2 format, chain N [auth E] MOL2 format, chain J [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth D] mmCIF format, chain P [auth F] mmCIF format, chain N [auth E] mmCIF format, chain J [auth C]	G [auth A] H [auth B] J [auth C] K [auth D] N [auth E] G [auth A], H [auth B], J [auth C], K [auth D], N [auth E], P [auth F]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain N [auth E] Focus chain P [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain N [auth E] Focus chain P [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth D] SDF format, chain O [auth E] MOL2 format, chain I [auth B] MOL2 format, chain L [auth D] MOL2 format, chain O [auth E] mmCIF format, chain I [auth B] mmCIF format, chain L [auth D] mmCIF format, chain O [auth E]	I [auth B], L [auth D], O [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Focus chain L [auth D] Focus chain O [auth E] Interactions & Density Focus chain I [auth B] Focus chain L [auth D] Focus chain O [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]