8QDF

Engineered LmrR with Met-89 replaced by para-boronophenylalanine

PDB DOI: https://doi.org/10.2210/pdb8QDF/pdb

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

Deposited: 2023-08-29 Released: 2024-05-01
Deposition Author(s): Thunnissen, A.M.W.H., Rozeboom, H.J., Longwitz, L., Leveson-Gower, R.B., Roelfes, G.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.277
R-Value Work: 0.206
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

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

Literature

Boron catalysis in a designed enzyme

Longwitz, L., Leveson-Gower, R.B., Rozeboom, H.J., Thunnissen, A.M.W.H., Roelfes, G.

To be published.

Macromolecule Content

Total Structure Weight: 59.3 kDa
Atom Count: 3,596
Modelled Residue Count: 423
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, PadR-like family	A, B, C, D	126	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

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
7N8 Query on 7N8	A, B, C, D	L-PEPTIDE LINKING	C₉ H₁₂ B N O₄		PHE

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.277
R-Value Work: 0.206
R-Value Observed: 0.210
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.674	α = 90
b = 53.89	β = 95.45
c = 69.034	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-01

Deposition Author(s):

Thunnissen, A.M.W.H.

Leveson-Gower, R.B.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	885396

Revision History (Full details and data files)

Version 1.0: 2024-05-01
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.