6WNI

Crystal structure of CldA, the first cyclomaltodextrin glucanotransferase with a three-domain ABC distribution

PDB DOI: https://doi.org/10.2210/pdb6WNI/pdb

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

Deposited: 2020-04-22 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: 1.66 Å
R-Value Free: 0.212
R-Value Work: 0.188
R-Value Observed: 0.190

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: 125.21 kDa
Atom Count: 9,091
Modelled Residue Count: 987
Deposited Residue Count: 1,070
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclomaltodextrin glucanotransferase	A, B	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	U5CJP3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain F [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	F [auth A], V [auth B], W [auth B], X [auth B]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain F [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [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] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] G [auth A] H [auth A] AA [auth B], BA [auth B], CA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], Y [auth B], Z [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	C [auth A] D [auth A] E [auth A] S [auth B] T [auth B] C [auth A], D [auth A], E [auth A], S [auth B], T [auth B], U [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.212
R-Value Work: 0.188
R-Value Observed: 0.190
Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.44	α = 90
b = 66.44	β = 90
c = 209.5	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

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