1ZY9 | pdb_00001zy9

Crystal structure of Alpha-galactosidase (EC 3.2.1.22) (Melibiase) (tm1192) from Thermotoga maritima at 2.34 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1ZY9/pdb

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


• Deposited: 2005-06-09 Released: 2005-07-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.213 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.171 (DCC) 

Literature

Crystal structure of alpha-galactosidase (ec 3.2.1.22) (melibiase) (tm1192) from Thermotoga maritima at 2.34 A resolution

Joint Center for Structural Genomics (JCSG)

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: 66.01 kDa 
• Atom Count: 4,524 
• Modeled Residue Count: 526 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-galactosidase	A	564	Thermotoga maritima	Mutation(s): 9  Gene Names: tm1192 EC: 3.2.1.22
UniProt
Find proteins for G4FEF4 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore G4FEF4  Go to UniProtKB:  G4FEF4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.213 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.171 (DCC) 

Diffraction Data: https://doi.org/10.18430/M31ZY9

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.729	α = 90
b = 160.533	β = 90
c = 88.258	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2005-07-12
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-16
  Changes: Data collection, Structure summary