2EKM | pdb_00002ekm

Structure of ST1219 protein from Sulfolobus tokodaii

• PDB DOI: https://doi.org/10.2210/pdb2EKM/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Sulfurisphaera tokodaii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-23 Released: 2008-03-25 
• Deposition Author(s): Lokanath, N.K., Pampa, K.J., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Structure of ST1219 protein from Sulfolobus tokodaii

Lokanath, N.K., Pampa, K.J., Kamiya, T., Kunishima, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 54.32 kDa 
• Atom Count: 4,201 
• Modeled Residue Count: 480 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ST1511	A, B, C	162	Sulfurisphaera tokodaii	Mutation(s): 0
UniProt
Find proteins for Q970U0 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q970U0  Go to UniProtKB:  Q970U0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.2	α = 90
b = 63.2	β = 90
c = 229.46	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Lokanath, N.K., Pampa, K.J., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description