4F8X | pdb_00004f8x

Penicillium canescens endo-1,4-beta-xylanase XylE

• PDB DOI: https://doi.org/10.2210/pdb4F8X/pdb

• Classification: HYDROLASE
• Organism(s): Penicillium canescens
• Expression System: Penicillium canescens
• Mutation(s): No 


• Deposited: 2012-05-18 Released: 2012-05-30 
• Deposition Author(s): Polyakov, K.M., Trofimov, A.A., Fedorova, T.V., Koroleva, O.V., Maisuradze, I.G., Chulkin, A.M., Vavilova, E.A., Benevolenskii, S.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.170 (Depositor), 0.167 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

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: 38.36 kDa 
• Atom Count: 3,069 
• Modeled Residue Count: 335 
• Deposited Residue Count: 335 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase	A	335	Penicillium canescens	Mutation(s): 0  Gene Names: xylE EC: 3.2.1.8
UniProt
Find proteins for C3VEV9 (Penicillium canescens) Explore C3VEV9  Go to UniProtKB:  C3VEV9
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G89225LT GlyCosmos: G89225LT GlyGen: G89225LT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.170 (Depositor), 0.167 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.23	α = 90
b = 60.29	β = 115.2
c = 55.62	γ = 90

Software Package:

Software Name	Purpose
AUTOMAR	data collection
BALBES	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Polyakov, K.M., Trofimov, A.A., Fedorova, T.V., Koroleva, O.V., Maisuradze, I.G., Chulkin, A.M., Vavilova, E.A., Benevolenskii, S.V.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary