1ZP6 | pdb_00001zp6

Crystal Structure of Atu3015, a Putative Cytidylate Kinase from Agrobacterium tumefaciens, Northeast Structural Genomics Target AtR62

• PDB DOI: https://doi.org/10.2210/pdb1ZP6/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-05-16 Released: 2005-05-24 
• Deposition Author(s): Forouhar, F., Abashidze, M., Vorobiev, S.M., Kuzin, A., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.322 (Depositor), 0.319 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.271 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Literature

Crystal Structure of Atu3015, a Putative Cytidylate Kinase from Agrobacterium tumefaciens, Northeast Structural Genomics Target AtR62

Forouhar, F., Abashidze, M., Vorobiev, S.M., Kuzin, A., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

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.

Macromolecule Content 

• Total Structure Weight: 21.21 kDa 
• Atom Count: 1,365 
• Modeled Residue Count: 176 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein Atu3015	A	191	Agrobacterium fabrum str. C58	Mutation(s): 2
UniProt
Find proteins for A9CEJ3 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CEJ3  Go to UniProtKB:  A9CEJ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.322 (Depositor), 0.319 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.271 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.96	α = 90
b = 91.96	β = 90
c = 173.603	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SDMS	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-24 
Deposition Author(s): Forouhar, F., Abashidze, M., Vorobiev, S.M., Kuzin, A., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2005-05-24
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2017-10-11
  Changes: Refinement description
• Version 1.5: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary