2FEX | pdb_00002fex

The Crystal Structure of DJ-1 Superfamily Protein Atu0886 from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb2FEX/pdb

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


• Deposited: 2005-12-16 Released: 2006-01-31 
• Deposition Author(s): Cymborowski, M.T., Wang, S., Chruszcz, M., Shumilin, I., Gu, J., Xu, X., Edwards, A.M., Savchenko, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.199 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

The Crystal Structure of DJ-1 Superfamily Protein Atu0886 from Agrobacterium tumefaciens

Cymborowski, M.T., Wang, S., Chruszcz, M., Shumilin, I., Gu, J., Xu, X., Edwards, A.M., Savchenko, A., Minor, W.

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)

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: 59.12 kDa 
• Atom Count: 4,945 
• Modelled Residue Count: 564 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved hypothetical protein	A, B, C	188	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: Atu0886
UniProt
Find proteins for A9CJS5 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CJS5  Go to UniProtKB:  A9CJS5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth B], F [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.70 Å
• R-Value Free:  0.199 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.411	α = 90
b = 89.411	β = 90
c = 163.486	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
Coot	model building
ARP/wARP	model building
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-31 
Deposition Author(s): Cymborowski, M.T., Wang, S., Chruszcz, M., Shumilin, I., Gu, J., Xu, X., Edwards, A.M., Savchenko, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-01-31
  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: 2011-10-05
  Changes: Structure summary
• Version 1.4: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary