9K2F | pdb_00009k2f

Crystal Structure of CyaF/SAH in open conformational state

PDB DOI: https://doi.org/10.2210/pdb9K2F/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Actinoalloteichus caeruleus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-17 Released: 2025-10-22
Deposition Author(s): Chen, R.J., Zhang, L.P., Zhu, Y.G., Zhang, C.S.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.278 (Depositor), 0.274 (DCC)
R-Value Work:
0.222 (Depositor), 0.225 (DCC)
R-Value Observed:
0.225 (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

The open conformation of CyaF, a N-methyltransferase Involved in Cyanogramide Biosynthesis

Chen, R.J., Zhang, L.P., Zhu, Y.G., Zhang, C.S.

To be published.

Macromolecule Content

Total Structure Weight: 57.18 kDa
Atom Count: 3,501
Modeled Residue Count: 456
Deposited Residue Count: 524
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CyaF	A [auth B], B [auth D]	262	Actinoalloteichus caeruleus	Mutation(s): 0
UniProt
Find proteins for A0A6M3FWK4 (Actinoalloteichus cyanogriseus) Explore A0A6M3FWK4 Go to UniProtKB: A0A6M3FWK4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6M3FWK4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 C [auth B] SDF format, chain D MOL2 format, chain C [auth B] MOL2 format, chain D mmCIF format, chain C [auth B] mmCIF format, chain D	C [auth B], D	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth B] Focus chain D Interactions & Density Focus chain C [auth B] Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.278 (Depositor), 0.274 (DCC)
R-Value Work: 0.222 (Depositor), 0.225 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.355	α = 90
b = 103.045	β = 90
c = 122.381	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22177119
National Natural Science Foundation of China (NSFC)	China	22193072

Revision History (Full details and data files)

Version 1.0: 2025-10-22
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.