8OZ8 | pdb_00008oz8

Crystal Structure of an Hydroxynitrile lyase variant (H96A) from Granulicella tundricola

PDB DOI: https://doi.org/10.2210/pdb8OZ8/pdb

Classification: LYASE
Organism(s): Granulicella tundricola
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-05-08 Released: 2024-04-10
Deposition Author(s): Bento, I., Coloma, J., Hagedoorn, P.-L., Hanefeld, U.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.195 (Depositor), 0.203 (DCC)
R-Value Work:
0.164 (Depositor), 0.174 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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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

Can a Hydroxynitrile Lyase Catalyze an Oxidative Cleavage?

Coloma, J., Hagedoorn, P.L., Bento, I., Hanefeld, U.

(2023) ACS Catal 13: 11182-11194

DOI: https://doi.org/10.1021/acscatal.3c02249

Macromolecule Content

Total Structure Weight: 58.55 kDa
Atom Count: 4,771
Modeled Residue Count: 524
Deposited Residue Count: 524
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin 2 conserved barrel domain protein	A, B, C, D	131	Granulicella tundricola	Mutation(s): 1 Gene Names: AciX9_0562 EC: 4.1.2.10
UniProt
Find proteins for E8WYN5 (Granulicella tundricola (strain ATCC BAA-1859 / DSM 23138 / MP5ACTX9)) Explore E8WYN5 Go to UniProtKB: E8WYN5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E8WYN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2PE Query on 2PE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PG5 Query on PG5 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C₈ H₁₈ O₄ YFNKIDBQEZZDLK-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
NM2 (Subject of Investigation/LOI) Query on NM2 Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], N [auth C], P [auth D]	3-CARBOXY-N,N,N-TRIMETHYLPROPAN-1-AMINIUM C₇ H₁₆ N O₂ JHPNVNIEXXLNTR-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain P [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain L [auth B] SDF format, chain K [auth B] MOL2 format, chain R [auth D] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] mmCIF format, chain R [auth D] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B]	K [auth B], L [auth B], R [auth D]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth D] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth D]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], O [auth C], Q [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain Q [auth D]