8KDL

Crystal structure of LmbF in complex with PLP

PDB DOI: https://doi.org/10.2210/pdb8KDL/pdb

Classification: LYASE
Organism(s): Streptomyces lincolnensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-09 Released: 2024-08-14
Deposition Author(s): Mori, T., Lyu, S., Kadlcik, S., Abe, I.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.204
R-Value Work: 0.165
R-Value Observed: 0.166

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of LmbF in complex with PLP

Mori, T., Lyu, S., Kadlcik, S., Abe, I.

To be published.

Macromolecule Content

Total Structure Weight: 96.93 kDa
Atom Count: 7,326
Modelled Residue Count: 823
Deposited Residue Count: 874
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme	A, B	437	Streptomyces lincolnensis	Mutation(s): 0 Gene Names: GJU35_01420
UniProt
Find proteins for A9Y8R7 (Streptomyces lincolnensis) Explore A9Y8R7 Go to UniProtKB: A9Y8R7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9Y8R7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B]	C [auth B], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

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: 1.70 Å
R-Value Free: 0.204
R-Value Work: 0.165
R-Value Observed: 0.166
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.277	α = 90
b = 74.017	β = 93.183
c = 74.843	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: 2024-08-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-08-14
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 R01GM133198.