2YYH | pdb_00002yyh

Crystal structure of Nudix family protein from Aquifex aeolicus

• PDB DOI: https://doi.org/10.2210/pdb2YYH/pdb

• Classification: HYDROLASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-30 Released: 2007-11-06 
• Deposition Author(s): Nakagawa, N., Kishishita, S., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.248 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal structure of Nudix family protein from Aquifex aeolicus

Nakakaga, N., Kishishita, S., Yokoyama, S., Kuramitsu, S.

To be published.

Biological Assembly 1  

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

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 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.22 kDa 
• Atom Count: 4,879 
• Modeled Residue Count: 548 
• Deposited Residue Count: 556 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
8-OXO-dGTPase domain	A, B, C, D	139	Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: mutT
UniProt
Find proteins for O67435 (Aquifex aeolicus (strain VF5)) Explore O67435  Go to UniProtKB:  O67435

Small Molecules

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: 1.80 Å
• R-Value Free:  0.248 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.02	α = 90
b = 34.336	β = 106.06
c = 130.005	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Nakagawa, N., Kishishita, S., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary