3AW9 | pdb_00003aw9

Structure of UDP-galactose 4-epimerase mutant

• PDB DOI: https://doi.org/10.2210/pdb3AW9/pdb

• Classification: ISOMERASE
• Organism(s): Pyrobaculum calidifontis JCM 11548
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-15 Released: 2012-02-29 
• Deposition Author(s): Sakuraba, H., Kawai, T., Yoneda, K., Ohshima, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Structure of UDP-galactose 4-epimerase mutant

Sakuraba, H., Kawai, T., Yoneda, K., Ohshima, T.

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: 105.28 kDa 
• Atom Count: 7,500 
• Modeled Residue Count: 903 
• Deposited Residue Count: 924 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent epimerase/dehydratase	A, B, C	308	Pyrobaculum calidifontis JCM 11548	Mutation(s): 0  Gene Names: Pcal_0885
UniProt
Find proteins for A3MUJ4 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1)) Explore A3MUJ4  Go to UniProtKB:  A3MUJ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], G [auth B], I [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GDU	D [auth A], F [auth B], H [auth C]	GALACTOSE-URIDINE-5'-DIPHOSPHATE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-ABVWGUQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.623	α = 90
b = 113.644	β = 90
c = 217.267	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Sakuraba, H., Kawai, T., Yoneda, K., Ohshima, T.

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2014-06-18
  Changes: Database references
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary