4XEA

Crystal structure of putative M16-like peptidase from Alicyclobacillus acidocaldarius

• PDB DOI: https://doi.org/10.2210/pdb4XEA/pdb

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


• Deposited: 2014-12-23 Released: 2015-03-18 
• Deposition Author(s): Michalska, K., Tesar, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.214 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Literature

Crystal structure of putative M16-like peptidase from Alicyclobacillus acidocaldarius

Michalska, K., Tesar, C., 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: 49.15 kDa 
• Atom Count: 3,580 
• Modelled Residue Count: 423 
• Deposited Residue Count: 423 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase M16 domain protein	A	423	Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446	Mutation(s): 0  Gene Names: Aaci_1020
UniProt
Find proteins for C8WVD6 (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 C8WVD6  Go to UniProtKB:  C8WVD6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NI	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-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: 1.95 Å
• R-Value Free: 0.214 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M34XEA

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.201	α = 90
b = 127.201	β = 90
c = 65.991	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
MLPHARE	phasing
HKL-3000	phasing
ARP	model building
SHELX	phasing
DM	phasing
HKL-3000	data reduction
WARP	model building
SHELX	model building
DM	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Michalska, K., Tesar, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary