3LU2 | pdb_00003lu2

Structure of lmo2462, a Listeria monocytogenes amidohydrolase family putative dipeptidase

• PDB DOI: https://doi.org/10.2210/pdb3LU2/pdb

• Classification: HYDROLASE
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-16 Released: 2010-03-09 
• Deposition Author(s): Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Hasseman, J., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.185 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

Structure of lmo2462, a Listeria monocytogenes amidohydrolase family putative dipeptidase

Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Hasseman, J., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.08 kDa 
• Atom Count: 5,254 
• Modeled Residue Count: 618 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo2462 protein	A, B	311	Listeria monocytogenes	Mutation(s): 0  Gene Names: lmo2462
UniProt
Find proteins for Q8Y4H9 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y4H9  Go to UniProtKB:  Q8Y4H9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth B], F [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: 2.20 Å
• R-Value Free:  0.185 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33lu2

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.088	α = 90
b = 179.088	β = 90
c = 46.412	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Hasseman, J., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-12-07
  Changes: Structure summary
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2018-01-31
  Changes: Database references
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary