9IIJ | pdb_00009iij

Engineered LmrR with V15 replaced by unnatural amino acid 4-amino-L-phenyl-cysteine

PDB DOI: https://doi.org/10.2210/pdb9IIJ/pdb

Classification: TRANSCRIPTION
Organism(s): Lactococcus cremoris subsp. cremoris MG1363
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-06-20 Released: 2025-06-25
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: 2.70 Å
R-Value Free:
0.286 (Depositor), 0.294 (DCC)
R-Value Work:
0.242 (Depositor), 0.248 (DCC)
R-Value Observed:
0.244 (Depositor)

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

Literature

Engineered 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: 14.14 kDa
Atom Count: 913
Modeled Residue Count: 110
Deposited Residue Count: 123
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, PadR-like family	A	123	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.286 (Depositor), 0.294 (DCC)
R-Value Work: 0.242 (Depositor), 0.248 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.62	α = 90
b = 70.62	β = 90
c = 61.33	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-25

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: 2025-06-25
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.