3NIX

Crystal structure of flavoprotein/dehydrogenase from Cytophaga hutchinsonii. Northeast Structural Genomics Consortium Target ChR43.

• PDB DOI: https://doi.org/10.2210/pdb3NIX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cytophaga hutchinsonii ATCC 33406
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-16 Released: 2010-06-30 
• Deposition Author(s): Vorobiev, S., Su, M., Seetharaman, J., Sahdev, S., Xiao, R., Foote, E.L., Ciccosanti, C., Maglaqui, M., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.264 
• R-Value Work: 0.237 
• R-Value Observed: 0.238 

Starting Model: experimental

Literature

Crystal structure of flavoprotein/dehydrogenase from Cytophaga hutchinsonii.

Vorobiev, S., Su, M., Seetharaman, J., Sahdev, S., Xiao, R., Foote, E.L., Ciccosanti, C., Maglaqui, M., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Biological Assembly 7  

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

Biological assembly 7 assigned by authors and generated by PISA (software)

Biological Assembly 8  

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

Biological assembly 8 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 389.76 kDa 
• Atom Count: 26,852 
• Modelled Residue Count: 3,232 
• Deposited Residue Count: 3,368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavoprotein/dehydrogenase	A, B, C, D, E, F, G, H	421	Cytophaga hutchinsonii ATCC 33406	Mutation(s): 0  Gene Names: CHU_2822, fixC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.264 
• R-Value Work: 0.237 
• R-Value Observed: 0.238 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.224	α = 90
b = 244.046	β = 104.1
c = 100.222	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Web-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing
PHENIX	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-30 
Deposition Author(s): Vorobiev, S., Su, M., Seetharaman, J., Sahdev, S., Xiao, R., Foote, E.L., Ciccosanti, C., Maglaqui, M., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2010-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-22
  Changes: Data collection
• Version 1.5: 2024-11-27
  Changes: Structure summary