5CQF

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.233
R-Value Work: 0.184
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

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

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q881D3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] 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		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.184
R-Value Observed: 0.186
Space Group: I 2 2 2
Diffraction Data: https://doi.org/10.18430/M35CQF

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

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Entry History & Funding Information

Deposition Data

Released Date: 2015-09-30

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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 (Full details and data files)

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

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Help and Resources

5CQF

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)