6WNU | pdb_00006wnu

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.227 (Depositor), 0.227 (DCC)
R-Value Work:
0.186 (Depositor), 0.186 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 (PDB Primary Data), 3.2.1.1 (UniProt)
UniProt
Find proteins for U5CJP3 (Caldanaerobacter subterraneus subsp. yonseiensis KB-1) Explore U5CJP3 Go to UniProtKB: U5CJP3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	U5CJP3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	I [auth A], J [auth A], K [auth A], L [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.227 (Depositor), 0.227 (DCC)
R-Value Work: 0.186 (Depositor), 0.186 (DCC)
R-Value Observed: 0.188 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-28

Deposition Author(s):

Magana-Cuevas, E.

Centeno-Leija, S.

Serrano-Posada, H.

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