8ZIJ | pdb_00008zij

The holo structure of gamma-lyase CndF

PDB DOI: https://doi.org/10.2210/pdb8ZIJ/pdb

Classification: LYASE
Organism(s): Penicillium citrinum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-14 Released: 2025-11-26
Deposition Author(s): Gao, Y., Tang, Y., Zhou, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free:
0.255 (Depositor), 0.256 (DCC)
R-Value Work:
0.214 (Depositor), 0.218 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure and Mechanism of the Pyridoxal 5'-Phosphate-Dependent Amino Acid gamma-Substitution Enzyme in 6-Alkyl-Pipecolate Biosynthesis

Gao, Y., Wang, B., Zhou, J., Gu, Y.

(2025) ACS Catal : 18893-18907

DOI: https://doi.org/10.1021/acscatal.5c04786

Macromolecule Content

Total Structure Weight: 126.69 kDa
Atom Count: 7,428
Modeled Residue Count: 949
Deposited Residue Count: 1,136
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLP dependent gamma-lyase CndF	A [auth B], B [auth A]	568	Penicillium citrinum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A [auth B], B [auth A]	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.255 (Depositor), 0.256 (DCC)
R-Value Work: 0.214 (Depositor), 0.218 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.432	α = 90
b = 102.527	β = 90
c = 128.124	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

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.