8W8U | pdb_00008w8u

High-resolution X-ray structure of cellulase Cel6A from Phanerochaete chrysosporium at cryogenic temperature

PDB DOI: https://doi.org/10.2210/pdb8W8U/pdb

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

Deposited: 2023-09-04 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: 0.80 Å
R-Value Free:
0.128 (Depositor), 0.129 (DCC)
R-Value Work:
0.116 (Depositor), 0.118 (DCC)

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: 38.91 kDa
Atom Count: 3,869
Modeled Residue Count: 358
Deposited Residue Count: 358
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H3K419
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.80 Å
R-Value Free: 0.128 (Depositor), 0.129 (DCC)
R-Value Work: 0.116 (Depositor), 0.118 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.926	α = 90
b = 67.018	β = 90
c = 88.25	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
SHELXL	refinement
XDS	data reduction

Structure Validation

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View more in-depth experimental data

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