3TP9 | pdb_00003tp9

Crystal structure of Alicyclobacillus acidocaldarius protein with beta-lactamase and rhodanese domains

• PDB DOI: https://doi.org/10.2210/pdb3TP9/pdb

• Classification: HYDROLASE
• Organism(s): Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-07 Released: 2011-09-21 
• Deposition Author(s): Michalska, K., Chhor, G., Mandel, M.E., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Crystal structure of Alicyclobacillus acidocaldarius protein with beta-lactamase and rhodanese domains

Michalska, K., Chhor, G., Mandel, M.E., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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)

Macromolecule Content 

• Total Structure Weight: 103.79 kDa 
• Atom Count: 7,256 
• Modeled Residue Count: 945 
• Deposited Residue Count: 948 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-LACTAMASE and RHODANESE DOMAIN PROTEIN	A, B	474	Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446	Mutation(s): 0  Gene Names: Aaci_0383
UniProt
Find proteins for C8WS08 (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 C8WS08  Go to UniProtKB:  C8WS08

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-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: 2.70 Å
• R-Value Free:  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33TP9

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.335	α = 90
b = 169.335	β = 90
c = 77.797	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
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
Deposition Author(s): Michalska, K., Chhor, G., Mandel, M.E., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-09-21
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary