2ZAC | pdb_00002zac

Crystal Structure of Family 7 Alginate Lyase A1-II' Y284F in Complex with Product (MMG)

• PDB DOI: https://doi.org/10.2210/pdb2ZAC/pdb

• Classification: LYASE
• Organism(s): Sphingomonas sp. A1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-10-02 Released: 2008-05-27 
• Deposition Author(s): Ogura, K., Yamasaki, M., Mikami, B., Hashimoto, W., Murata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Substrate Recognition in Tunnel of Family 7 Alginate Lyase from Sphingomonas sp. A1

Ogura, K., Yamasaki, M., Mikami, B., Hashimoto, W., 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: 26.42 kDa 
• Atom Count: 2,183 
• Modeled Residue Count: 227 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alginate lyase	A	236	Sphingomonas sp. A1	Mutation(s): 1  Gene Names: aly EC: 4.2.2.3
UniProt
Find proteins for Q75WP3 (Sphingomonas sp. A1) Explore Q75WP3  Go to UniProtKB:  Q75WP3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid	B	3	N/A	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.935	α = 90
b = 68.884	β = 90
c = 80.433	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., Mikami, B., Hashimoto, W., 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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2021-11-10
  Changes: Data collection, Database references, Structure summary
• Version 2.2: 2023-11-01
  Changes: Data collection, Refinement description