3X2M

X-ray structure of PcCel45A with cellopentaose at 0.64 angstrom resolution.

• PDB DOI: https://doi.org/10.2210/pdb3X2M/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., Samejima, M., Igarashi, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.64 Å
• R-Value Free: 0.129 
• R-Value Work: 0.122 
• R-Value Observed: 0.122 

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: 19.84 kDa 
• Atom Count: 1,811 
• Modelled 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	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	5		N/A
Glycosylation Resources
GlyTouCan:  G75287MT GlyCosmos:  G75287MT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C	5		N/A
Glycosylation Resources
GlyTouCan:  G91683DU GlyCosmos:  G91683DU

Biologically Interesting Molecules (External Reference) 1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.64 Å
• R-Value Free: 0.129 
• R-Value Work: 0.122 
• R-Value Observed: 0.122 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.938	α = 90
b = 57.554	β = 90
c = 63.431	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Nakamura, A., Ishida, T., 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: 2015-12-30
  Changes: Experimental preparation
• Version 1.3: 2019-12-18
  Changes: Data collection, 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