2Z42

Crystal Structure of Family 7 Alginate Lyase A1-II' from Sphingomonas sp. A1

• PDB DOI: https://doi.org/10.2210/pdb2Z42/pdb

• Classification: LYASE
• Organism(s): Sphingomonas sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-06-12 Released: 2008-05-27 
• Deposition Author(s): Ogura, K., Yamasaki, M., Hashimoto, W., Mikami, B., Murata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Substrate Recognition by Family 7 Alginagte Lyase from Sphingomonas sp. A1

Ogura, K., Yamasaki, M., Hashimoto, W., Mikami, B., Murata, K.

To be published.

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: 26.21 kDa 
• Atom Count: 2,105 
• Modelled Residue Count: 233 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alginate lyase	A	237	Sphingomonas sp.	Mutation(s): 0  Gene Names: aly EC: 4.2.2.3
UniProt
Find proteins for Q75WP3 (Sphingomonas sp. A1) Explore Q75WP3  Go to UniProtKB:  Q75WP3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.335	α = 90
b = 41.329	β = 90
c = 133.378	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Ogura, K., Yamasaki, M., Hashimoto, W., Mikami, B., Murata, K.

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2016-12-21
  Changes: Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description