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

Find similar proteins by:

(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] mmCIF 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] mmCIF format, chain B [auth A] mmCIF 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

View Full Validation Report

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