8X00 | pdb_00008x00

X-Ray crystal structure of glycoside hydrolase family 6 cellobiohydrolase from Phanerochaete chrysosporium PcCel6A C240S/C393S/D394C

PDB DOI: https://doi.org/10.2210/pdb8X00/pdb

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

Deposited: 2023-11-02 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: 1.53 Å
R-Value Free:
0.196 (Depositor), 0.196 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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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: 38.81 kDa
Atom Count: 3,464
Modeled Residue Count: 358
Deposited Residue Count: 358
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucanase	A	358	Phanerodontia chrysosporium	Mutation(s): 3 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02321
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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	B	2		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS Query on OCS	A	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.196 (Depositor), 0.196 (DCC)
R-Value Work: 0.166 (Depositor), 0.166 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.69	α = 90
b = 67.49	β = 90
c = 88	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.