1WE5 | pdb_00001we5

Crystal Structure of Alpha-Xylosidase from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb1WE5/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-05-24 Released: 2005-02-15 
• Deposition Author(s): Ose, T., Kitamura, M., Okuyama, M., Mori, H., Kimura, A., Watanabe, N., Yao, M., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.247 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 

Literature

Crystal Structure of Alpha-Xylosidase from Escherichia coli

Ose, T., Kitamura, M., Okuyama, M., Mori, H., Kimura, A., Watanabe, N., Yao, M., Tanaka, I.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 535.56 kDa 
• Atom Count: 37,302 
• Modeled Residue Count: 4,557 
• Deposited Residue Count: 4,632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative family 31 glucosidase yicI	A, B, C, D, E, F	772	Escherichia coli	Mutation(s): 19  Gene Names: YicI EC: 3.2.1 (PDB Primary Data), 3.2.1.177 (UniProt)
UniProt
Find proteins for P31434 (Escherichia coli (strain K12)) Explore P31434  Go to UniProtKB:  P31434

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.247 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.337	α = 90
b = 174.791	β = 90
c = 209.629	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement
SnB	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-15 
Deposition Author(s): Ose, T., Kitamura, M., Okuyama, M., Mori, H., Kimura, A., Watanabe, N., Yao, M., Tanaka, I.

Revision History  

• Version 1.0: 2005-02-15
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary