3QSJ | pdb_00003qsj

Crystal structure of NUDIX hydrolase from Alicyclobacillus acidocaldarius

• PDB DOI: https://doi.org/10.2210/pdb3QSJ/pdb

• Classification: HYDROLASE
• Organism(s): Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-02-21 Released: 2011-04-13 
• Deposition Author(s): Michalska, K., Wu, R., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.205 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of NUDIX hydrolase from Alicyclobacillus acidocaldarius

Michalska, K., Wu, R., Bearden, J., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.43 kDa 
• Atom Count: 1,958 
• Modeled Residue Count: 222 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUDIX hydrolase	A	232	Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446	Mutation(s): 0  Gene Names: Aaci_1025
UniProt
Find proteins for C8WVE1 (Alicyclobacillus acidocaldarius subsp. acidocaldarius (strain ATCC 27009 / DSM 446 / BCRC 14685 / JCM 5260 / KCTC 1825 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-IA)) Explore C8WVE1  Go to UniProtKB:  C8WVE1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	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:  0.205 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.844	α = 90
b = 82.152	β = 90
c = 36.614	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
Coot	model building
PHENIX	refinement
BUSTER	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-13 
Deposition Author(s): Michalska, K., Wu, R., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-04-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary