2YZJ | pdb_00002yzj

Crystal structure of dCTP deaminase from Sulfolobus tokodaii

• PDB DOI: https://doi.org/10.2210/pdb2YZJ/pdb

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


• Deposited: 2007-05-06 Released: 2007-11-06 
• Deposition Author(s): Kanagawa, M., Baba, S., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.227 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Crystal structure of dCTP deaminase from Sulfolobus tokodaii

Kanagawa, M., Baba, S., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G.

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: 58.93 kDa 
• Atom Count: 4,135 
• Modeled Residue Count: 474 
• Deposited Residue Count: 507 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
167aa long hypothetical dUTPase	A, B, C	169	Sulfurisphaera tokodaii	Mutation(s): 0  EC: 3.6.1.23
UniProt
Find proteins for F9VNI5 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore F9VNI5  Go to UniProtKB:  F9VNI5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUD	D [auth A], I [auth B], J [auth C]	DEOXYURIDINE-5'-DIPHOSPHATE C9 H14 N2 O11 P2 QHWZTVCCBMIIKE-SHYZEUOFSA-N
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MG	F [auth B], G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.227 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.77	α = 107.47
b = 53.757	β = 107.52
c = 53.757	γ = 107.5

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Kanagawa, M., Baba, S., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Data collection
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary