6ILB | pdb_00006ilb

Native crystal structure of fructuronate-tagaturonate epimerase UxaE from Cohnella laeviribosi

• PDB DOI: https://doi.org/10.2210/pdb6ILB/pdb

• Classification: ISOMERASE
• Organism(s): Cohnella laeviribosi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-17 Released: 2019-10-23 
• Deposition Author(s): Choi, M.Y., Kang, L.W., Ho, T.H., Nguyen, D.Q., Lee, I.H., Lee, J.H., Park, Y.S., Park, H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of fructuronate-tagaturonate epimerase UxaE from Cohnella laeviribosi

Choi, M.Y., Kang, L.W., Ho, T.H., Nguyen, D.Q., Lee, I.H., Lee, J.H., Park, Y.S., Park, H.J.

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)

Macromolecule Content 

• Total Structure Weight: 110.91 kDa 
• Atom Count: 7,805 
• Modeled Residue Count: 980 
• Deposited Residue Count: 980 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructuronate-tagaturonate epimerase UxaE from Cohnella laeviribosi in complex with 1 glycerol	A	490	Cohnella laeviribosi	Mutation(s): 0  EC: 5.1.2.7
UniProt
Find proteins for A0A6D2YCT9 (Cohnella laeviribosi) Explore A0A6D2YCT9  Go to UniProtKB:  A0A6D2YCT9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructuronate-tagaturonate epimerase UxaE from Cohnella laeviribosi in complex with 1 glycerol	B [auth D]	490	Cohnella laeviribosi	Mutation(s): 0  EC: 5.1.2.7
UniProt
Find proteins for A0A6D2YCT9 (Cohnella laeviribosi) Explore A0A6D2YCT9  Go to UniProtKB:  A0A6D2YCT9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth M], F [auth M]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C, D [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.816	α = 98.135
b = 73.47	β = 110.157
c = 74.673	γ = 90.119

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-23 
Deposition Author(s): Choi, M.Y., Kang, L.W., Ho, T.H., Nguyen, D.Q., Lee, I.H., Lee, J.H., Park, Y.S., Park, H.J.

Revision History  

• Version 1.0: 2019-10-23
  Type: Initial release
  
• Version 2.0: 2024-10-23
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary