8X0I | pdb_00008x0i

X-Ray crystal structure of glycoside hydrolase family 6 cellobiohydrolase from Phanerochaete chrysosporium PcCel6A C240S/C393S soaked in cellobioimidazole

PDB DOI: https://doi.org/10.2210/pdb8X0I/pdb

Classification: HYDROLASE
Organism(s): Phanerodontia chrysosporium
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2023-11-04 Released: 2024-11-20
Deposition Author(s): Yamaguchi, S., Sunagawa, N., Tachioka, M., Igarashi, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free:
0.149 (Depositor), 0.149 (DCC)
R-Value Work:
0.136 (Depositor), 0.136 (DCC)
R-Value Observed:
0.137 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Activity and X-ray crystal structure of candidate base catalyst mutants of glycoside hydrolase family 6 cellobiohydrolase

Yamaguchi, S., Sunagawa, N., Tachioka, M., Igarashi, K.

To be published.

Macromolecule Content

Total Structure Weight: 38.71 kDa
Atom Count: 4,407
Modeled Residue Count: 358
Deposited Residue Count: 358
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucanase	A	358	Phanerodontia chrysosporium	Mutation(s): 2 Gene Names: cel6A EC: 3.2.1
UniProt
Find proteins for Q02321 (Phanerodontia chrysosporium) Explore Q02321 Go to UniProtKB: Q02321
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02321
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IDC (Subject of Investigation/LOI) Query on IDC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl beta-D-glucopyranoside C₁₄ H₂₂ N₂ O₉ CSXOUJBOYXGFCL-OFKZETBZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free: 0.149 (Depositor), 0.149 (DCC)
R-Value Work: 0.136 (Depositor), 0.136 (DCC)
R-Value Observed: 0.137 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.825	α = 90
b = 67.239	β = 90
c = 88.36	γ = 90

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

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22J12651

Revision History (Full details and data files)

Version 1.0: 2024-11-20
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.