5CQF | pdb_00005cqf

Crystal structure of L-lysine 6-monooxygenase from Pseudomonas syringae

• PDB DOI: https://doi.org/10.2210/pdb5CQF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas syringae pv. tomato str. DC3000
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-21 Released: 2015-09-30 
• Deposition Author(s): Michalska, K., Bigelow, L., Jedrzejczak, R., Weerth, R.S., Cao, H., Yennamalli, R., Phillips Jr., G.N., Thomas, M.G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.233 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Crystal structure of L-lysine 6-monooxygenase from Pseudomonas syringae

Michalska, K., Bigelow, L., Jedrzejczak, R., Weerth, R.S., Cao, H., Yennamalli, R., Phillips Jr., G.N., Thomas, M.G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.81 kDa 
• Atom Count: 3,398 
• Modeled Residue Count: 419 
• Deposited Residue Count: 443 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lysine 6-monooxygenase	A	443	Pseudomonas syringae pv. tomato str. DC3000	Mutation(s): 0  Gene Names: PSPTO_2961
UniProt
Find proteins for Q881D3 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q881D3  Go to UniProtKB:  Q881D3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.233 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35CQF

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.218	α = 90
b = 85.495	β = 90
c = 139.016	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Michalska, K., Bigelow, L., Jedrzejczak, R., Weerth, R.S., Cao, H., Yennamalli, R., Phillips Jr., G.N., Thomas, M.G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U01GM098248

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Structure summary