2DGD | pdb_00002dgd

Crystal structure of ST0656, a function unknown protein from Sulfolobus tokodaii

• PDB DOI: https://doi.org/10.2210/pdb2DGD/pdb

• Classification: LYASE
• Organism(s): Sulfurisphaera tokodaii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-03-10 Released: 2007-03-13 
• Deposition Author(s): Tanaka, Y., Sasaki, T., Tanabe, E., Yao, M., Tanaka, I., Kumagai, I., Tsumoto, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal structure of ST0656, a function unknown protein from Sulfolobus tokodaii

Tanaka, Y., Sasaki, T., Tanabe, E., Yao, M., Tanaka, I., Kumagai, I., Tsumoto, K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 103.27 kDa 
• Atom Count: 7,376 
• Modeled Residue Count: 888 
• Deposited Residue Count: 892 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
223aa long hypothetical arylmalonate decarboxylase	A, B, C, D	223	Sulfurisphaera tokodaii	Mutation(s): 6  EC: 4.1.1.76
UniProt
Find proteins for Q974K3 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q974K3  Go to UniProtKB:  Q974K3

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.221	α = 90
b = 131.221	β = 90
c = 125.896	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-13 
Deposition Author(s): Tanaka, Y., Sasaki, T., Tanabe, E., Yao, M., Tanaka, I., Kumagai, I., Tsumoto, K.

Revision History  

• Version 1.0: 2007-03-13
  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: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary