1B3V

XYLANASE FROM PENICILLIUM SIMPLICISSIMUM, COMPLEX WITH XYLOSE

• PDB DOI: https://doi.org/10.2210/pdb1B3V/pdb

• Classification: FAMILY 10 XYLANASE
• Organism(s): Penicillium simplicissimum
• Mutation(s): No 


• Deposited: 1998-12-15 Released: 1999-04-07 
• Deposition Author(s): Schmidt, A., Kratky, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.274 
• R-Value Work: 0.211 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.17 kDa 
• Atom Count: 2,564 
• Modelled Residue Count: 302 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (XYLANASE)	A	302	Penicillium simplicissimum	Mutation(s): 0  EC: 3.2.1.8
UniProt
Find proteins for P56588 (Penicillium simplicissimum) Explore P56588  Go to UniProtKB:  P56588

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYS	D [auth A]	alpha-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-LECHCGJUSA-N
XYP	B [auth A], C [auth A], E [auth A]	beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.274 
• R-Value Work: 0.211 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.86	α = 90
b = 81.86	β = 90
c = 113.59	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-07 
Deposition Author(s): Schmidt, A., Kratky, C.

Revision History  

• Version 1.0: 1999-04-07
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2019-12-25
  Changes: Data collection, Database references, Derived calculations, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-08-09
  Changes: Data collection, Database references, Refinement description, Structure summary