8Y8M | pdb_00008y8m

Crystal structure of a benzaldehyde lyase mutant M3 from Herbiconiux sp. SALV-R1

PDB DOI: https://doi.org/10.2210/pdb8Y8M/pdb

Classification: LYASE
Organism(s): Herbiconiux sp. SALV-R1
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2024-02-06 Released: 2025-02-12
Deposition Author(s): Li, Y., Zhang, Y.F., Chen, Y.Y., Liu, W.D., Yao, P.Y., Wu, Q.Q., Zhu, D.M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.209 (Depositor), 0.216 (DCC)
R-Value Work:
0.180 (Depositor), 0.189 (DCC)
R-Value Observed:
0.181 (Depositor)

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

Ligand Structure Quality Assessment

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

Literature

Manipulating Activity and Chemoselectivity of a Benzaldehyde Lyase for Efficient Synthesis of alpha-Hydroxymethyl Ketones and One-Pot Enantio-Complementary Conversion to 1,2-Diols

Zhang, Y., Li, Y., Chen, Y., Liu, W., Zhao, Q., Feng, J., Yao, P., Wu, Q., Zhu, D.

(2024) ACS Catal 14: 9687-9700

DOI: https://doi.org/10.1021/acscatal.4c01804

Macromolecule Content

Total Structure Weight: 59.68 kDa
Atom Count: 4,427
Modeled Residue Count: 552
Deposited Residue Count: 558
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine pyrophosphate-binding protein	A	558	Herbiconiux sp. SALV-R1	Mutation(s): 3 Gene Names: HL652_19860
UniProt
Find proteins for A0A6M5J4S0 (Herbiconiux sp. SALV-R1) Explore A0A6M5J4S0 Go to UniProtKB: A0A6M5J4S0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6M5J4S0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP (Subject of Investigation/LOI) Query on TPP Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]