Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 39.77 kDa 
• Atom Count: 3336 
• Modelled Residue Count: 353 
• Deposited Residue Count: 355 
• Unique protein chains: 1

3A71

High resolution structure of Penicillium chrysogenum alpha-L-arabinanase

• PDB DOI: 10.2210/pdb3A71/pdb

• Classification: HYDROLASE
• Organism(s): Penicillium chrysogenum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-11 Released: 2010-09-15 
• Deposition Author(s): Sogabe, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 0.128 
• R-Value Observed: 0.107 

Literature

High-resolution structure of exo-arabinanase from Penicillium chrysogenum

Sogabe, Y., Kitatani, T., Yamaguchi, A., Kinoshita, T., Adachi, H., Takano, K., Inoue, T., Mori, Y., Matsumura, H., Sakamoto, T., Tada, T.

(2011) Acta Crystallogr D Biol Crystallogr 67: 415-422

• PubMed: 21543843 
• DOI: 10.1107/S0907444911006299
• Primary Citation of Related Structures:  
  3A71, 3A72


• PubMed Abstract: 
  

Arabinanase Abnx from Penicillium chrysogenum 31B, which belongs to the GH93 family, releases arabinobiose from the nonreducing terminus of α-1,5-L-arabinan, which is distributed in the primary cell walls of higher plants. Crystal structures of Abnx and of its complex with arabinobiose were determined at the high resolutions of 1.14 Å to an R(work) of 10.7% (R(free) = 12.8%) and 1.04 Å to an R(work) of 10.4% (R(free) = 12.5%). Abnx has a six-bladed β-propeller fold with a typical ring-closure mode called `Velcro', in which the last four-stranded β-sheet is completed by the incorporation of a strand from the N-terminus. Catalytic residues which act as a nucleophile and an acid/base were proposed from the structures and confirmed by site-directed mutagenesis. The substrate-binding groove is enclosed at one end by two residues, Glu64 and Tyr66, which contribute to the recognition of the nonreducing chain end of the polysaccharide. A comparison with the related enzyme Arb93A which has a quite similar overall structure suggested that Abnx has different mechanisms to funnel substrates to the active site and/or to stabilize the transition state.

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Organizational Affiliation: 

Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exo-arabinanase	A	355	Penicillium chrysogenum	Mutation(s): 0  Gene Names: abnx EC: 3.2.1.55
UniProt
Find proteins for Q7ZA77 (Penicillium chrysogenum) Explore Q7ZA77  Go to UniProtKB:  Q7ZA77

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth A], E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 0.128 
• R-Value Observed: 0.107 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.877	α = 90
b = 77.248	β = 90
c = 79.441	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-09-11 
• Released Date: 2010-09-15 
Deposition Author(s): Sogabe, Y.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance