8ZIF | pdb_00008zif

Gamma-lyase CndF in complex with pyridoxal 5'-phosphate, L-homoserine and ethyl acetoacetate

PDB DOI: https://doi.org/10.2210/pdb8ZIF/pdb

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

Deposited: 2024-05-13 Released: 2025-11-19
Deposition Author(s): Gao, Y., Zhou, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.265 (Depositor), 0.262 (DCC)
R-Value Work:
0.238 (Depositor), 0.240 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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: 126.8 kDa
Atom Count: 7,216
Modeled Residue Count: 926
Deposited Residue Count: 1,136
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLP dependent gamma-lyase CndF	A, B	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
EAC (Subject of Investigation/LOI) Query on EAC 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]	ethyl 3-oxobutanoate C₆ H₁₀ O₃ XYIBRDXRRQCHLP-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
HSE (Subject of Investigation/LOI) Query on HSE Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	L-HOMOSERINE C₄ H₉ N O₃ UKAUYVFTDYCKQA-VKHMYHEASA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.265 (Depositor), 0.262 (DCC)
R-Value Work: 0.238 (Depositor), 0.240 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.709	α = 90
b = 100.65	β = 90
c = 129.076	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-11-19
Type: Initial release
Version 1.1: 2025-11-26
Changes: Database references

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.