5I1W

Crystal structure of CrmK, a flavoenzyme involved in the shunt product recycling mechanism in caerulomycin biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb5I1W/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Actinoalloteichus sp. WH1-2216-6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-07 Released: 2017-02-15 
• Deposition Author(s): Picard, M.-E., Barma, J., Shi, R.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.213 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Biochemical and structural insights into flavoenzyme CrmK reveals a shunt product recycling mechanism in caerulomycin biosynthesis

Zhu, Y., Picard, M.-E., Mei, X., Zhang, Q., Barma, J., Murphy Despres, X., Couture, M., Zhu, W., Zhang, C., Shi, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 225.09 kDa 
• Atom Count: 16,449 
• Modelled Residue Count: 1,992 
• Deposited Residue Count: 2,000 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CrmK	A, B, C, D	500	Actinoalloteichus sp. WH1-2216-6	Mutation(s): 0
UniProt
Find proteins for H8Y6P5 (Actinoalloteichus sp. WH1-2216-6) Explore H8Y6P5  Go to UniProtKB:  H8Y6P5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], G [auth B], I [auth C], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
67L	F [auth A], H [auth B], J [auth C]	6-(hydroxymethyl)[2,2'-bipyridin]-4-ol C11 H10 N2 O2 HKHZGZONLACWBE-UHFFFAOYSA-N
67K	L [auth D]	4-hydroxy[2,2'-bipyridine]-6-carbaldehyde C11 H8 N2 O2 FFOWHRKNAPHKGV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.213 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.11	α = 94.73
b = 95.2	β = 96.56
c = 98.04	γ = 105.2

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Picard, M.-E., Barma, J., Shi, R.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary