1X1N | pdb_00001x1n

Structure determination and refinement at 1.8 A resolution of Disproportionating Enzyme from Potato

• PDB DOI: https://doi.org/10.2210/pdb1X1N/pdb

• Classification: TRANSFERASE
• Organism(s): Solanum tuberosum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-04-08 Released: 2006-04-18 
• Deposition Author(s): Imamura, K., Matsuura, T., Takaha, T., Fujii, K., Nakagawa, A., Kusunoki, M., Nitta, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.210 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structure determination and refinement at 1.8 A resolution of Disproportionating Enzyme from Potato

Imamura, K., Matsuura, T., Takaha, T., Fujii, K., Nakagawa, A., Kusunoki, M., Nitta, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 60.09 kDa 
• Atom Count: 4,941 
• Modeled Residue Count: 523 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-alpha-glucanotransferase	A	524	Solanum tuberosum	Mutation(s): 0  EC: 2.4.1.25
UniProt
Find proteins for Q06801 (Solanum tuberosum) Explore Q06801  Go to UniProtKB:  Q06801

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.210 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.869	α = 90
b = 120.535	β = 90
c = 174.382	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-18 
Deposition Author(s): Imamura, K., Matsuura, T., Takaha, T., Fujii, K., Nakagawa, A., Kusunoki, M., Nitta, Y.

Revision History  

• Version 1.0: 2006-04-18
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description