3PVZ | pdb_00003pvz

UDP-N-acetylglucosamine 4,6-dehydratase from Vibrio fischeri

• PDB DOI: https://doi.org/10.2210/pdb3PVZ/pdb
• Entry: 3PVZ supersedes: 3NZO

• Classification: LYASE
• Organism(s): Aliivibrio fischeri ES114
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-12-07 Released: 2011-01-12 
• Deposition Author(s): Osipiuk, J., Marshall, N., Tesar, C., Pearson, L., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.233 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

UDP-N-acetylglucosamine 4,6-dehydratase from Vibrio fischeri.

Osipiuk, J., Marshall, N., Tesar, C., Pearson, L., 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)

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: 187.55 kDa 
• Atom Count: 12,086 
• Modeled Residue Count: 1,414 
• Deposited Residue Count: 1,596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine 4,6-dehydratase	A, B, C, D	399	Aliivibrio fischeri ES114	Mutation(s): 0  Gene Names: VF_0140 EC: 4.2.1
UniProt
Find proteins for Q5E8L1 (Aliivibrio fischeri (strain ATCC 700601 / ES114)) Explore Q5E8L1  Go to UniProtKB:  Q5E8L1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], K [auth B], L [auth C], N [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SCN	F [auth A], G [auth A], M [auth C], O [auth D], P [auth D]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
NA	H [auth A], I [auth A], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.233 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.92	α = 102.71
b = 74.837	β = 95.15
c = 88.789	γ = 100.35

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-12 
Deposition Author(s): Osipiuk, J., Marshall, N., Tesar, C., Pearson, L., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 3NZO

Revision History  

• Version 1.0: 2011-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary