2DDX | pdb_00002ddx

Crystal structure of beta-1,3-xylanase from Vibrio sp. AX-4

• PDB DOI: https://doi.org/10.2210/pdb2DDX/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio sp. AX-4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-02-06 Released: 2007-02-13 
• Deposition Author(s): Sakaguchi, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.86 Å
• R-Value Free: 
  0.148 (Depositor), 0.156 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Literature

Atomic resolution analysis of beta-1,3-xylanase catalytic module from Vibrio sp. AX-4

Sakaguchi, K., Kawamura, T., Watanabe, N., Kiyohara, M., Yamaguchi, K., Ito, M., Tanaka, I.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.24 kDa 
• Atom Count: 3,033 
• Modeled Residue Count: 324 
• Deposited Residue Count: 333 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-1,3-xylanase	A	333	Vibrio sp. AX-4	Mutation(s): 0  EC: 3.2.1 (PDB Primary Data), 3.2.1.32 (UniProt)
UniProt
Find proteins for D5MP61 (Vibrio sp) Explore D5MP61  Go to UniProtKB:  D5MP61

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.86 Å
• R-Value Free:  0.148 (Depositor), 0.156 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.873	α = 90
b = 75.654	β = 90
c = 82.119	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-13 
Deposition Author(s): Sakaguchi, K.

Revision History  

• Version 1.0: 2007-02-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary