3DB9 | pdb_00003db9

Crystal structure of UPF0317 protein Atu3911 from Agrobacterium tumefaciens. NorthEast Strcutural Genomics target AtR186

• PDB DOI: https://doi.org/10.2210/pdb3DB9/pdb

• Classification: structural genomics, unknown function
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-30 Released: 2008-07-29 
• Deposition Author(s): Seetharaman, J., Abashidze, M., Wang, D., Janjua, H., Owens, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.268 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of UPF0317 protein Atu3911 from Agrobacterium tumefaciens. NorthEast Strcutural Genomics target AtR186 (CASP Target)

Seetharaman, J., Abashidze, M., Wang, D., Janjua, H., Owens, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, 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 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.97 kDa 
• Atom Count: 1,885 
• Modeled Residue Count: 235 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0317 protein Atu3911	A	269	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: Atu3911, AGR_L_1868 EC: 4.2.1
UniProt
Find proteins for Q8U919 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q8U919  Go to UniProtKB:  Q8U919

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.268 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.374	α = 90
b = 101.374	β = 90
c = 84.325	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-29 
Deposition Author(s): Seetharaman, J., Abashidze, M., Wang, D., Janjua, H., Owens, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2008-07-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Refinement description