1ORU | pdb_00001oru

Crystal Structure of APC1665, YUAD protein from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb1ORU/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-03-15 Released: 2003-09-23 
• Deposition Author(s): Kim, Y., Joachimiak, A., Edwards, A., Skarina, T., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.225 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Crystal Structure of APC1665, YUAD protein from Bacillus subtilis

Kim, Y., Joachimiak, A., Edwards, A., Skarina, T., Savchenko, 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: 44.17 kDa 
• Atom Count: 3,312 
• Modeled Residue Count: 364 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
yuaD protein	A, B	195	Bacillus subtilis	Mutation(s): 6
UniProt
Find proteins for O32079 (Bacillus subtilis (strain 168)) Explore O32079  Go to UniProtKB:  O32079

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A], E [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.80 Å
• R-Value Free:  0.225 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.652	α = 90
b = 87.202	β = 90
c = 122.249	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
d*TREK	data reduction
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-23 
Deposition Author(s): Kim, Y., Joachimiak, A., Edwards, A., Skarina, T., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2003-09-23
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary