6THM | pdb_00006thm

Linalool Dehydratase Isomerase M125A mutant

PDB DOI: https://doi.org/10.2210/pdb6THM/pdb

Classification: LYASE
Organism(s): Castellaniella defragrans 65Phen
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-11-20 Released: 2020-10-07
Deposition Author(s): Cuetos, A., Zukic, E., Danesh-Azari, H.R., Grogan, G.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.215 (Depositor), 0.222 (DCC)
R-Value Work:
0.178 (Depositor), 0.186 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Mutational Analysis of Linalool Dehydratase Isomerase Suggests That Alcohol and Alkene Transformations Are Catalyzed Using Noncovalent Mechanisms

Cuetos, A., Iglesias-Fernandez, J., Danesh-Azari, H.R., Zukic, E., Dowle, A., Osuna, S., Grogan, G.

(2020) ACS Catal

DOI: https://doi.org/10.1021/acscatal.0c02958

Macromolecule Content

Total Structure Weight: 210.8 kDa
Atom Count: 15,330
Modeled Residue Count: 1,825
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Linalool dehydratase-isomerase protein LDI	A, B, C, D, E	372	Castellaniella defragrans 65Phen	Mutation(s): 1 Gene Names: BN940_14136 EC: 5.4.4.4 (UniProt), 4.2.1.127 (UniProt)
UniProt
Find proteins for E1XUJ2 (Castellaniella defragrans (strain DSM 12143 / CCUG 39792 / 65Phen)) Explore E1XUJ2 Go to UniProtKB: E1XUJ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E1XUJ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain L [auth B] MOL2 format, chain V [auth E] MOL2 format, chain L [auth B] mmCIF format, chain V [auth E] mmCIF format, chain L [auth B]	L [auth B], V [auth E]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain L [auth B] Focus chain V [auth E] Interactions & Density Focus chain L [auth B] Focus chain V [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth B] J [auth B] F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth D], R [auth E], S [auth E], T [auth E], U [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.215 (Depositor), 0.222 (DCC)
R-Value Work: 0.178 (Depositor), 0.186 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.67	α = 90
b = 110.689	β = 91.26
c = 196.715	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-10-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/P005578/1

Revision History (Full details and data files)

Version 1.0: 2020-10-07
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary