2I3D | pdb_00002i3d

Crystal Structure of Protein of Unknown Function ATU1826, a Putative Alpha/Beta Hydrolase from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb2I3D/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-08-17 Released: 2006-09-19 
• Deposition Author(s): Osipiuk, J., Xu, X., Zheng, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.174 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Literature

Crystal structure of hypothetical protein Atu1826, a putative alpha/beta hydrolase from Agrobacterium tumefaciens.

Osipiuk, J., Xu, X., Zheng, H., 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: 56.54 kDa 
• Atom Count: 4,127 
• Modeled Residue Count: 438 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein Atu1826	A, B	249	Agrobacterium fabrum str. C58	Mutation(s): 6  Gene Names: Atu1826
UniProt
Find proteins for A9CIK7 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CIK7  Go to UniProtKB:  A9CIK7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.174 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.549	α = 92.25
b = 50.579	β = 115.17
c = 54.844	γ = 99.82

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-19 
Deposition Author(s): Osipiuk, J., Xu, X., Zheng, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-09-19
  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: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary