8YRF | pdb_00008yrf

Crystal structure of LmrR with V15 replaced by unnatural amino acid 4-amino-L-phenyl-cysteine

• PDB DOI: https://doi.org/10.2210/pdb8YRF/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Lactococcus cremoris subsp. cremoris MG1363
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-03-21 Released: 2024-04-24 
• Deposition Author(s): Zhou, Z., Huang, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.274 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of LmrR with V15 replaced by unnatural amino acid 4-amino-L-phenyl-cysteine

Zhou, Z., Huang, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.3 kDa 
• Atom Count: 1,809 
• Modeled Residue Count: 218 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, PadR-like family	A, B	131	Lactococcus cremoris subsp. cremoris MG1363	Mutation(s): 1  Gene Names: llmg_0323
UniProt
Find proteins for A2RI36 (Lactococcus lactis subsp. cremoris (strain MG1363)) Explore A2RI36  Go to UniProtKB:  A2RI36

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1D64	A, B	L-PEPTIDE LINKING	C9 H12 N2 O2 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.274 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.31	α = 90
b = 63.31	β = 90
c = 63.92	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
ADDREF	data reduction
SCALA	data scaling
ACORN	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Zhou, Z., Huang, W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22207043

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release