3X2P | pdb_00003x2p

Neutron and X-ray joint refined structure of PcCel45A with cellopentaose at 298K.

• PDB DOI: https://doi.org/10.2210/pdb3X2P/pdb

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


• Deposited: 2014-12-22 Released: 2015-10-14 
• Deposition Author(s): Nakamura, A., Ishida, T., Kusaka, K., Yamada, T., Tanaka, I., Niimura, N., Samejima, M., Igarashi, K.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.260 (Depositor) 
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.219 (Depositor) 

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• Method: X-RAY DIFFRACTION
• Resolution: 0.99 Å
• R-Value Free: 
  0.142 (Depositor), 0.143 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Literature

"Newton's cradle" proton relay with amide-imidic acid tautomerization in inverting cellulase visualized by neutron crystallography.

Nakamura, A., Ishida, T., Kusaka, K., Yamada, T., Fushinobu, S., Tanaka, I., Kaneko, S., Ohta, K., Tanaka, H., Inaka, K., Higuchi, Y., Niimura, N., Samejima, M., Igarashi, K.

(2015) Sci Adv 1: e1500263-e1500263

• PubMed: 26601228 
• DOI: https://doi.org/10.1126/sciadv.1500263
• Primary Citation Related Structures: 
  3X2G, 3X2H, 3X2I, 3X2J, 3X2K, 3X2L, 3X2M, 3X2N, 3X2O, 3X2P, 4ZM7


• PubMed Abstract: 
  

  Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase PcCel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium. Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the "Newton's cradle"-like proton relay pathway of the catalytic cycle. Amide-imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions.

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Organizational Affiliation: 
• Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.
Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Ibaraki 319-1106, Japan.
Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.
Department of Subtropical Biochemistry and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Okinawa 903-0213, Japan.
Japanese Experiment Module (JEM) Utilization Center, Japan Aerospace Exploration Agency, Ibaraki 305-8505, Japan.
Confocal Science Inc., Tokyo 101-0032, Japan.
Maruwa Foods and Biosciences Inc., Nara 639-1123, Japan.
Department of Life Science, University of Hyogo, Hyogo 678-1297, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.01 kDa 
• Atom Count: 1,589 
• Modeled Residue Count: 180 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase V-like protein	A	180	Phanerodontia chrysosporium	Mutation(s): 0  Gene Names: egv, PcCel45A
UniProt
Find proteins for B3Y002 (Phanerodontia chrysosporium) Explore B3Y002  Go to UniProtKB:  B3Y002

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	5		N/A
Glycosylation Resources
GlyTouCan: G91683DU GlyCosmos: G91683DU

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
41Q	A	L-PEPTIDE LINKING	C4 H8 N2 O3		ASN

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900016	B	beta-cellopentaose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.260 (Depositor) 
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.219 (Depositor) 

• Method: X-RAY DIFFRACTION
• Resolution: 0.99 Å
• R-Value Free:  0.142 (Depositor), 0.143 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.478	α = 90
b = 58.635	β = 90
c = 64.744	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
STARGazer	data reduction
STARGazer	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Nakamura, A., Ishida, T., Kusaka, K., Yamada, T., Tanaka, I., Niimura, N., Samejima, M., Igarashi, K.

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2015-11-04
  Changes: Other
• Version 1.2: 2018-03-07
  Changes: Data collection
• Version 1.3: 2018-05-16
  Changes: Data collection
• Version 1.4: 2019-12-18
  Changes: Database references, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2025-03-26
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2025-10-29
  Changes: Data collection