5L9C | pdb_00005l9c

Crystal structure of an endoglucanase from Penicillium verruculosum in complex with cellobiose

PDB DOI: https://doi.org/10.2210/pdb5L9C/pdb

Classification: HYDROLASE
Organism(s): Talaromyces verruculosus
Expression System: Talaromyces verruculosus
Mutation(s): No

Deposited: 2016-06-10 Released: 2017-06-28
Deposition Author(s): Nemashkalov, V., Vakhrusheva, A., Tishchenko, S., Gabdulkhakov, A., Kravchenko, O., Gusakov, A., Sinisyn, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.273 (Depositor), 0.274 (DCC)
R-Value Work:
0.226 (Depositor), 0.227 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of an endoglucanase from Penicillium verruculosum in complex with cellobiose

Nemashkalov, V., Vakhrusheva, A., Tishchenko, S., Gabdulkhakov, A., Kravchenko, O., Gusakov, A., Sinisyn, A.

To be published.

Macromolecule Content

Total Structure Weight: 143.04 kDa
Atom Count: 11,348
Modeled Residue Count: 1,216
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): 0 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	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Interactions & Density Focus chain E Focus chain F Focus chain G
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	H, I, J, K, L H, I, J, K, L, M, N, O	2		N/A	Interactions Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Interactions & Density Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O
Glycosylation Resources
GlyTouCan: G84824ZO GlyCosmos: G84824ZO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C]	P [auth C], Q [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain P [auth C] Focus chain Q [auth C]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005 Query on PRD_900005	H, I, J, K, L H, I, J, K, L, M, N, O	beta-cellobiose	Oligosaccharide / Metabolism		Interactions Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Interactions & Density Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.273 (Depositor), 0.274 (DCC)
R-Value Work: 0.226 (Depositor), 0.227 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.33	α = 87.23
b = 73.23	β = 94.17
c = 91.15	γ = 100.52

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	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: 2017-06-28

Deposition Author(s):

Funding Organization	Location	Grant Number
	Russian Federation	--

Revision History (Full details and data files)

Version 1.0: 2017-06-28
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary