2G84 | pdb_00002g84

Cytidine and deoxycytidylate deaminase zinc-binding region from Nitrosomonas europaea.

• PDB DOI: https://doi.org/10.2210/pdb2G84/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Nitrosomonas europaea ATCC 19718
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-03-01 Released: 2006-04-04 
• Deposition Author(s): Osipiuk, J., Skarina, T., Onopriyenko, O., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.160 (Depositor), 0.159 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.126 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

Literature

X-ray crystal structure of Cytidine and deoxycytidylate deaminase zinc-binding region from Nitrosomonas europaea.

Osipiuk, J., Skarina, T., Onopriyenko, O., Savchenko, A., Edwards, A., Joachimiak, A.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.67 kDa 
• Atom Count: 3,327 
• Modeled Residue Count: 371 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytidine and deoxycytidylate deaminase zinc-binding region	A, B	197	Nitrosomonas europaea ATCC 19718	Mutation(s): 0  Gene Names: NE0047
UniProt
Find proteins for Q82Y41 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82Y41  Go to UniProtKB:  Q82Y41

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	E [auth A], J [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.160 (Depositor), 0.159 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.126 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.354	α = 90
b = 73.789	β = 90
c = 110.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
SCALEPACK	data scaling
SHELXD	phasing
CNS	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-04 
Deposition Author(s): Osipiuk, J., Skarina, T., Onopriyenko, O., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-04-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-03-10
  Changes: Advisory, Database references, Derived calculations
• Version 1.4: 2023-12-06
  Changes: Data collection, Database references, Derived calculations