5I3T | pdb_00005i3t

Native Structure of the Linalool Dehydratase-Isomerase from Castellaniella defragrans

PDB DOI: https://doi.org/10.2210/pdb5I3T/pdb

Classification: LYASE, ISOMERASE
Organism(s): Castellaniella defragrans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-02-11 Released: 2016-06-01
Deposition Author(s): LaMattina, J.W., Carlock, M., Koch, D.J., Lanzilotta, W.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.204 (Depositor), 0.207 (DCC)
R-Value Work:
0.163 (Depositor), 0.171 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Native Structure of the Linalool Dehydratase-Isomerase from Castellaniella defragrans

LaMattina, J.W., Carlock, M., Koch, D.J., Lanzilotta, W.N.

To be published.

Macromolecule Content

Total Structure Weight: 223.17 kDa
Atom Count: 15,049
Modeled Residue Count: 1,812
Deposited Residue Count: 1,985
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Linalool dehydratase/isomerase	A, B, C, D, E	397	Castellaniella defragrans	Mutation(s): 0 Gene Names: ldi EC: 4.2.1.127 (PDB Primary Data), 5.4.4.4 (PDB Primary Data)
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BU2 Query on BU2 Download:Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain L [auth D] SDF format, chain F [auth A] MOL2 format, chain P [auth E] MOL2 format, chain L [auth D] MOL2 format, chain F [auth A] mmCIF format, chain P [auth E] mmCIF format, chain L [auth D] mmCIF format, chain F [auth A]	F [auth A], L [auth D], P [auth E]	1,3-BUTANEDIOL C₄ H₁₀ O₂ PUPZLCDOIYMWBV-BYPYZUCNSA-N		Interactions Focus chain F [auth A] Focus chain L [auth D] Focus chain P [auth E] Interactions & Density Focus chain F [auth A] Focus chain L [auth D] Focus chain P [auth E]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain R [auth E] SDF format, chain O [auth D] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain R [auth E] MOL2 format, chain O [auth D] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain R [auth E] mmCIF format, chain O [auth D] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A], J [auth B], O [auth D], R [auth E]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain O [auth D] Focus chain R [auth E] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain O [auth D] Focus chain R [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth E] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A] I [auth B] K [auth C] M [auth D] N [auth D] G [auth A], I [auth B], K [auth C], M [auth D], N [auth D], Q [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain Q [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain Q [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.204 (Depositor), 0.207 (DCC)
R-Value Work: 0.163 (Depositor), 0.171 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.957	α = 90
b = 106.757	β = 90
c = 188.872	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-06-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-01
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary