4KVQ

Crystal Structure of Prochlorococcus marinus aldehyde-deformylating oxygenase wild type with palmitic acid bound

PDB DOI: https://doi.org/10.2210/pdb4KVQ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Prochlorococcus marinus str. MIT 9313
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-23 Released: 2013-06-26
Deposition Author(s): Levy, C.W., Khara, B., Menon, N., Mansell, D., Das, D., Marsh, E.N.G., Leys, D., Scrutton, N.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.217
R-Value Work: 0.178
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Production of propane and other short-chain alkanes by structure-based engineering of ligand specificity in aldehyde-deformylating oxygenase.

Khara, B., Menon, N., Levy, C., Mansell, D., Das, D., Marsh, E.N., Leys, D., Scrutton, N.S.

(2013) Chembiochem 14: 1204-1208

PubMed: 23757044 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/cbic.201300307
Primary Citation of Related Structures:
4KVQ, 4KVR, 4KVS

PubMed Abstract:
Biocatalytic propane production: structure-based engineering of aldehyde-deformylating oxygenase improves specificity for short- and medium-chain-length aldehydes and enhances the propane generation in whole-cell biotransformations. This presents new opportunities for developing biocatalytic modules for the production of volatile "drop-in" biofuels.

Organizational Affiliation

Manchester Institute of Biotechnology and Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.

Macromolecule Content

Total Structure Weight: 27.63 kDa
Atom Count: 2,064
Modelled Residue Count: 223
Deposited Residue Count: 244
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde decarbonylase	A	244	Prochlorococcus marinus str. MIT 9313	Mutation(s): 0 Gene Names: PMT_1231 EC: 4.1.99.5
UniProt
Find proteins for Q7V6D4 (Prochlorococcus marinus (strain MIT 9313)) Explore Q7V6D4 Go to UniProtKB: Q7V6D4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7V6D4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.217
R-Value Work: 0.178
R-Value Observed: 0.180
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.03	α = 90
b = 77.03	β = 90
c = 115.86	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-06-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-06-26
Type: Initial release
Version 1.1: 2013-08-28
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations