4WOQ | pdb_00004woq

Crystal Structures of CdNal from Clostridium difficile in complex with ketobutyric

• PDB DOI: https://doi.org/10.2210/pdb4WOQ/pdb

• Classification: LYASE
• Organism(s): Clostridioides difficile NAP08
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-16 Released: 2015-10-21 
• Deposition Author(s): Liu, W.D., Guo, R.T., Cui, Y.F., Chen, X., Wu, Q.Q., Zhu, D.M.
• Funding Organization(s): National Natural Science Foundation of China, National Basic Research Program of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

Crystal Structures of CdNal from Clostridium difficile in complex with ketobutyric

Liu, W.D., Guo, R.T., Cui, Y.F., Chen, X., Wu, Q.Q., Zhu, D.M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 275.77 kDa 
• Atom Count: 20,222 
• Modeled Residue Count: 2,320 
• Deposited Residue Count: 2,416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylneuraminate lyase	A, B, C, D, E, F, G, H	302	Clostridioides difficile NAP08	Mutation(s): 0  Gene Names: CdNal EC: 4.1.3.3
UniProt
Find proteins for D5Q364 (Clostridioides difficile NAP08) Explore D5Q364  Go to UniProtKB:  D5Q364

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2KT	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	2-KETOBUTYRIC ACID C4 H6 O3 TYEYBOSBBBHJIV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.875	α = 90
b = 122.612	β = 95.72
c = 122.186	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Liu, W.D., Guo, R.T., Cui, Y.F., Chen, X., Wu, Q.Q., Zhu, D.M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	21072151
National Natural Science Foundation of China	China	21102100
National Basic Research Program of China	China	2011CB710801

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection