4M82

The structure of E292S glycosynthase variant of exo-1,3-beta-glucanase from Candida albicans complexed with p-nitrophenyl-gentiobioside (product) at 1.6A resolution

PDB DOI: https://doi.org/10.2210/pdb4M82/pdb

Classification: HYDROLASE
Organism(s): Candida albicans SC5314
Expression System: Komagataella phaffii GS115
Mutation(s): Yes

Deposited: 2013-08-12 Released: 2014-06-25
Deposition Author(s): Nakatani, Y., Cutfield, S.M., Larsen, D.S., Cutfield, J.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.184
R-Value Work: 0.147
R-Value Observed: 0.149

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 46.46 kDa
Atom Count: 3,797
Modelled Residue Count: 393
Deposited Residue Count: 399
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXO-1,3-BETA-GLUCANASE	A	399	Candida albicans SC5314	Mutation(s): 1 Gene Names: CaO19.10507, XOG, XOG1 EC: 3.2.1.58
UniProt
Find proteins for P29717 (Candida albicans (strain SC5314 / ATCC MYA-2876)) Explore P29717 Go to UniProtKB: P29717
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29717
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NGB Query on NGB Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	4-nitrophenyl 6-O-beta-D-glucopyranosyl-beta-D-glucopyranoside C₁₈ H₂₅ N O₁₃ ISCYUJSLZREARS-NNUBVHJDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.184
R-Value Work: 0.147
R-Value Observed: 0.149
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.785	α = 90
b = 64.333	β = 90
c = 94.489	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-06-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-06-25
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

4M82

The structure of E292S glycosynthase variant of exo-1,3-beta-glucanase from Candida albicans complexed with p-nitrophenyl-gentiobioside (product) at 1.6A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)