8W4X | pdb_00008w4x

Neutron structure of cellulase Cel6A from Phanerochaete chrysosporium at room temperature, Enzyme-Product complex

PDB DOI: https://doi.org/10.2210/pdb8W4X/pdb

Classification: HYDROLASE
Organism(s): Phanerodontia chrysosporium
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2023-08-25 Released: 2025-03-12
Deposition Author(s): Tachioka, M., Yamaguchi, S., Nakamura, A., Ishida, T., Kusaka, K., Yamada, T., Yano, N., Chatake, T., Tamada, T., Takeda, K., Niwa, S., Tanaka, H., Takahashi, S., Inaka, K., Furubayashi, N., Deguchi, S., Samejima, M., Igarashi, K.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.139 (Depositor), 0.139 (DCC)
R-Value Work:
0.128 (Depositor), 0.127 (DCC)
R-Value Observed:
0.128 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.166 (Depositor)
R-Value Work:
0.147 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Deprotonated Arginine Controls a Putative Catalytic Base in Invert-ing Family 6 Glycoside Hydrolase

Tachioka, M., Yamaguchi, S., Nakamura, A., Ishida, T., Kusaka, K., Yamada, T., Yano, N., Chatake, T., Tamada, T., Takeda, K., Niwa, S., Tanaka, H., Takahashi, S., Inaka, K., Furubayashi, N., Deguchi, S., Samejima, M., Igarashi, K.

To be published.

Macromolecule Content

Total Structure Weight: 38.93 kDa
Atom Count: 3,143
Modeled Residue Count: 358
Deposited Residue Count: 358
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucanase	A	358	Phanerodontia chrysosporium	Mutation(s): 0 Gene Names: cel6A EC: 3.2.1
UniProt
Find proteins for H3K419 (Phanerodontia chrysosporium) Explore H3K419 Go to UniProtKB: H3K419
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	H3K419
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B [auth C]	2	N/A	N/A	Interactions Focus chain B [auth C]
Glycosylation Resources
GlyTouCan: G86802XL GlyCosmos: G86802XL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC (Subject of Investigation/LOI) Query on BGC Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain C [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900023 Query on PRD_900023	B [auth C]	alpha-cellobiose	Oligosaccharide / Metabolism		Interactions Focus chain B [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.139 (Depositor), 0.139 (DCC)
R-Value Work: 0.128 (Depositor), 0.127 (DCC)
R-Value Observed: 0.128 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.166 (Depositor)
R-Value Work: 0.147 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.73	α = 90
b = 68.26	β = 90
c = 89.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
STARGazer	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	18H05494
Japan Society for the Promotion of Science (JSPS)	Japan	23H00341, 19H03013, 18J01906, 15J10657