6YON | pdb_00006yon

Crystal structure of Endoglucanase S127C/A165C from Penicillium verruculosum

PDB DOI: https://doi.org/10.2210/pdb6YON/pdb

Classification: HYDROLASE
Organism(s): Talaromyces verruculosus
Expression System: Penicillium canescens
Mutation(s): Yes

Deposited: 2020-04-14 Released: 2021-04-28
Deposition Author(s): Nemashkalov, V., Kravchenko, O., Gabdulkhakov, A., Tischenko, S., Rozhkova, A., Sinitsyn, A.
Funding Organization(s): Russian Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.292 (Depositor), 0.294 (DCC)
R-Value Work:
0.236 (Depositor), 0.243 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Endoglucanase S127C/A165C from Penicillium verruculosum

Nemashkalov, V., Kravchenko, O., Gabdulkhakov, A., Tischenko, S., Rozhkova, A., Sinitsyn, A.

To be published.

Macromolecule Content

Total Structure Weight: 140.86 kDa
Atom Count: 9,645
Modeled Residue Count: 1,220
Deposited Residue Count: 1,256
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase	A, B, C, D	314	Talaromyces verruculosus	Mutation(s): 4 EC: 3.2.1.4
UniProt
Find proteins for A0A1U7Q1U3 (Talaromyces verruculosus) Explore A0A1U7Q1U3 Go to UniProtKB: A0A1U7Q1U3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1U7Q1U3
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A], J [auth B], K [auth C], L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.292 (Depositor), 0.294 (DCC)
R-Value Work: 0.236 (Depositor), 0.243 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.5	α = 90
b = 85.69	β = 89.99
c = 91.15	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	--

Revision History (Full details and data files)

Version 1.0: 2021-04-28
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary