3NEH | pdb_00003neh

Crystal structure of the protein LMO2462 from Listeria monocytogenes complexed with ZN and phosphonate mimic of dipeptide L-Leu-D-Ala

• PDB DOI: https://doi.org/10.2210/pdb3NEH/pdb

• Classification: LYASE
• Organism(s): Listeria monocytogenes serotype 4b str. F2365
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-08 Released: 2010-06-30 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Cummings, J., Raushel, F.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.219 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the protein LMO2462 from Listeria monocytogenes complexed with ZN and phosphonate mimic of dipeptide L-Leu-D-Ala

Fedorov, A.A., Fedorov, E.V., Cummings, J., Raushel, F.M., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.01 kDa 
• Atom Count: 5,326 
• Modeled Residue Count: 618 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Renal dipeptidase family protein	A, B	318	Listeria monocytogenes serotype 4b str. F2365	Mutation(s): 0  Gene Names: LMOf2365_2435 EC: 4.99.1.1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L3A	C [auth A], F [auth B]	(2R)-3-[(R)-[(1R)-1-amino-3-methylbutyl](hydroxy)phosphoryl]-2-methylpropanoic acid C9 H20 N O4 P PYHFMEIRRPJIRC-JGVFFNPUSA-N
ZN	D [auth A], E [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.219 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.834	α = 90
b = 79.453	β = 90
c = 152.014	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-30 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Cummings, J., Raushel, F.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Advisory, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-06
  Changes: Advisory, Data collection, Database references, Refinement description