6WNU

Crystal structure of the three-domain cyclomaltodextrin glucanotransferase CldA in the monomeric form

• PDB DOI: https://doi.org/10.2210/pdb6WNU/pdb

• Classification: TRANSFERASE
• Organism(s): Caldanaerobacter subterraneus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-04-23 Released: 2021-04-28 
• Deposition Author(s): Magana-Cuevas, E., Centeno-Leija, S., Serrano-Posada, H.
• Funding Organization(s): Consejo Nacional de Ciencia y Tecnologia (CONACYT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.227 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Discovery of a novel group of three-domain thermophilic cyclomaltodextrin glucanotransferases: structural and functional implications.

Centeno-Leija, S., Lopez-Munguia, A., Cardenas-Conejo, Y., Mancilla-Margalli, N.A., Velazquez-Cruz, B., Magana-Cuevas, E., Guerra-Borrego, Y., Zatarain-Palacios, R., Marin-Tovar, Y., Gomez-Manzo, S., Marcial-Quino, J., Hernandez-Ochoa, B., Osuna-Castro, J.A., Rudino-Pinera, E., Serrano-Posada, H.

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 Evidence: light scattering, gel filtration

Macromolecule Content

• Total Structure Weight: 61.98 kDa 
• Atom Count: 4,498 
• Modelled Residue Count: 494 
• Deposited Residue Count: 535 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclomaltodextrin glucanotransferase	A	535	Caldanaerobacter subterraneus	Mutation(s): 0  Gene Names: O163_00610 EC: 2.4.1.19
UniProt
Find proteins for U5CJP3 (Caldanaerobacter subterraneus subsp. yonseiensis KB-1) Explore U5CJP3  Go to UniProtKB:  U5CJP3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	I [auth A], J [auth A], K [auth A], L [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT	E [auth A], F [auth A], G [auth A], H [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.227 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.77	α = 90
b = 67.77	β = 90
c = 105.1	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-04-28 
Deposition Author(s): Magana-Cuevas, E., Centeno-Leija, S., Serrano-Posada, H.

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Funding Organization	Location	Grant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)	Mexico	CB-2018-A1-S-18011
Consejo Nacional de Ciencia y Tecnologia (CONACYT)	Mexico	CB-2016-01-285001
Consejo Nacional de Ciencia y Tecnologia (CONACYT)	Mexico	INFR-2017-01-280608

Revision History  

• Version 1.0: 2021-04-28
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description