9LLS | pdb_00009lls

Crystal structure of Ornithine decarboxylase H346A mutant

PDB DOI: https://doi.org/10.2210/pdb9LLS/pdb

Classification: LYASE
Organism(s): Lacticaseibacillus rhamnosus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-01-17 Released: 2025-12-24
Deposition Author(s): Kim, D.S., Park, J.H., Adiko, N.N., Seo, H.T.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free:
0.231 (Depositor), 0.232 (DCC)
R-Value Work:
0.171 (Depositor), 0.182 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Insight into the functional and structural relationship of ornithine decarboxylase and its mutants from Lacticaseibacillus rhamnosus.

Adiko, N.N., Seo, H.T., Ki, D.W., Park, J.H., Kim, D.S.

(2025) Bull Korean Chem Soc 46: 730-742

DOI: https://doi.org/10.1002/bkcs.70035

Macromolecule Content

Total Structure Weight: 151.52 kDa
Atom Count: 10,709
Modeled Residue Count: 1,386
Deposited Residue Count: 1,388
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine decarboxylase	A, B	694	Lacticaseibacillus rhamnosus	Mutation(s): 1 Gene Names: LRHMDP2_881 EC: 4.1.1.17

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free: 0.231 (Depositor), 0.232 (DCC)
R-Value Work: 0.171 (Depositor), 0.182 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.364	α = 114.65
b = 72.38	β = 107.28
c = 78.05	γ = 100.49

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History (Full details and data files)

Version 1.0: 2025-12-24
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.