3NKL | pdb_00003nkl

Crystal Structure of UDP-D-Quinovosamine 4-Dehydrogenase from Vibrio fischeri

• PDB DOI: https://doi.org/10.2210/pdb3NKL/pdb

• Classification: oxidoreductase/lyase
• Organism(s): Aliivibrio fischeri ES114
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-06-20 Released: 2010-08-18 
• Deposition Author(s): Kim, Y., Mack, J., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.195 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Crystal Structure of UDP-D-Quinovosamine 4-Dehydrogenase from Vibrio fischeri

Kim, Y., Mack, J., Buck, K., Joachimiak, A.

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)

Macromolecule Content 

• Total Structure Weight: 32.28 kDa 
• Atom Count: 2,278 
• Modeled Residue Count: 245 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-D-quinovosamine 4-dehydrogenase	A, B	141	Aliivibrio fischeri ES114	Mutation(s): 0  Gene Names: VF_0197 EC: 1.1.1 (PDB Primary Data), 4.2.1 (PDB Primary Data)
UniProt
Find proteins for Q5E8F4 (Aliivibrio fischeri (strain ATCC 700601 / ES114)) Explore Q5E8F4  Go to UniProtKB:  Q5E8F4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], E [auth A], G [auth A], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	F [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.195 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.262	α = 90
b = 45.379	β = 91.54
c = 69.813	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
BUCCANEER	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BUCCANEER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Kim, Y., Mack, J., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary