8YRF

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free: 0.274
R-Value Work: 0.227
R-Value Observed: 0.229

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

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

Zhou, Z., Huang, W.

To be published.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2RI36
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1D64 Query on 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
R-Value Work: 0.227
R-Value Observed: 0.229
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

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Entry History & Funding Information

Deposition Data

Released Date: 2024-04-24

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2024-04-24
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.