4A7P | pdb_00004a7p

Se-Met derivatized UgdG, UDP-glucose dehydrogenase from Sphingomonas elodea

• PDB DOI: https://doi.org/10.2210/pdb4A7P/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sphingomonas elodea
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-14 Released: 2012-11-21 
• Deposition Author(s): Rocha, J., Granja, A.T., Sa-Correia, I., Fialho, A.M., Frazao, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.454 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.454 (DCC) 

Literature

The Structure of Ugdg, an Udp-Glucose Dehydrogenase from Sphingomonas Elodea Atcc 31461

Rocha, J., Granja, A.T., Sa-Correia, I., Fialho, A.M., Frazao, C.

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: 98.23 kDa 
• Atom Count: 6,557 
• Modeled Residue Count: 858 
• Deposited Residue Count: 892 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-GLUCOSE DEHYDROGENASE	A, B	446	Sphingomonas elodea	Mutation(s): 0  EC: 1.1.1.22
UniProt
Find proteins for A4UTT2 (Sphingomonas elodea) Explore A4UTT2  Go to UniProtKB:  A4UTT2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

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: 3.40 Å
• R-Value Free:  0.454 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.454 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.03	α = 90
b = 109.03	β = 90
c = 175.813	γ = 90

Software Package:

Software Name	Purpose
FFFEAR	model building
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
DM	phasing
RESOLVE	phasing
FFFEAR	phasing
XFIT	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-21 
Deposition Author(s): Rocha, J., Granja, A.T., Sa-Correia, I., Fialho, A.M., Frazao, C.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2017-07-12
  Changes: Refinement description
• Version 1.2: 2019-03-06
  Changes: Data collection, Derived calculations, Experimental preparation
• Version 1.3: 2019-09-25
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary