4KVS | pdb_00004kvs

Crystal Structure of Prochlorococcus marinus aldehyde-deformylating oxygenase (mutant A134F)

• PDB DOI: https://doi.org/10.2210/pdb4KVS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Prochlorococcus marinus str. MIT 9313
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.185 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

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 
• DOI: https://doi.org/10.1002/cbic.201300307
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.57 kDa 
• Atom Count: 2,080 
• Modeled Residue Count: 221 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde decarbonylase	A	244	Prochlorococcus marinus str. MIT 9313	Mutation(s): 1  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6NA	B [auth A]	HEXANOIC ACID C6 H12 O2 FUZZWVXGSFPDMH-UHFFFAOYSA-N
FE	C [auth A], D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.185 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.06	α = 90
b = 77.06	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

Entry History 

Deposition Data

• Released Date: 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.

Revision History  

• 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