4KCF | pdb_00004kcf

X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose

• PDB DOI: https://doi.org/10.2210/pdb4KCF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Actinomadura kijaniata
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-04-24 Released: 2013-05-22 
• Deposition Author(s): Holden, H.M., Thoden, J.B., Branch, M.C., Zimmer, A.L., Bruender, N.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.225 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Active site architecture of a sugar N-oxygenase.

Thoden, J.B., Branch, M.C., Zimmer, A.L., Bruender, N.A., Holden, H.M.

(2013) Biochemistry 52: 3191-3193

• PubMed: 23621882 
• DOI: https://doi.org/10.1021/bi400407x
• Primary Citation Related Structures: 
  4KCF


• PubMed Abstract: 
  

  KijD3 is a flavin-dependent N-oxygenase implicated in the formation of the nitro-containing sugar d-kijanose, found attached to the antibiotic kijanimicin. For this investigation, the structure of KijD3 in complex with FMN and its dTDP-sugar substrate was solved to 2.1 Å resolution. In contrast to the apoenzyme structure, the C-terminus of the protein becomes ordered and projects into the active site cleft [Bruender, N. A., Thoden, J. B., and Holden, H. M. (2010) Biochemistry 49, 3517-3524]. The amino group of the dTDP-aminosugar that is oxidized is located 4.9 Å from C4a of the flavin ring. The model provides a molecular basis for understanding the manner in which KijD3 catalyzes its unusual chemical transformation.

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Organizational Affiliation: 
• Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.35 kDa 
• Atom Count: 3,199 
• Modeled Residue Count: 407 
• Deposited Residue Count: 454 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD-dependent oxidoreductase	A	454	Actinomadura kijaniata	Mutation(s): 0  Gene Names: KijD3
UniProt
Find proteins for B3TMR1 (Actinomadura kijaniata) Explore B3TMR1  Go to UniProtKB:  B3TMR1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKM	B [auth A]	[(2R,4S,6R)-4-azanyl-4,6-dimethyl-5,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate C17 H29 N3 O14 P2 GACNZVKWDHTCBB-HHMBNNFFSA-N
FMN	C [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.225 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.828	α = 90
b = 81.297	β = 90
c = 152.628	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-22 
Deposition Author(s): Holden, H.M., Thoden, J.B., Branch, M.C., Zimmer, A.L., Bruender, N.A.

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2013-05-29
  Changes: Atomic model, Non-polymer description
• Version 1.2: 2013-12-18
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description