3TB5

Crystal Structure of the Enterococcus faecalis Methionine aminopeptidase apo form

• PDB DOI: https://doi.org/10.2210/pdb3TB5/pdb

• Classification: HYDROLASE
• Organism(s): Enterococcus faecalis HIP11704
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-05 Released: 2012-08-08 
• Deposition Author(s): Kishor, C., Gumpena, R., Reddi, R., Addlagatta, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.255 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 

Literature

Structural studies of Enterococcus faecalis methionine aminopeptidase and design of microbe specific 2,2'-bipyridine based inhibitors

Kishor, C., Gumpena, R., Reddi, R., Addlagatta, A.

(2012) Medchemcomm 3: 1406-1412

• DOI: https://doi.org/10.1039/c2md20096a

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 88.73 kDa 
• Atom Count: 5,897 
• Modelled Residue Count: 715 
• Deposited Residue Count: 792 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase	A, B, C	264	Enterococcus faecalis HIP11704	Mutation(s): 0  Gene Names: EFHG_00941, MetAP EC: 3.4.11.18

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	D [auth A], E [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.255 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.74	α = 90
b = 132.13	β = 133.36
c = 85.3	γ = 90

Software Package:

Software Name	Purpose
APEX	data collection
MOLREP	phasing
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-08 
Deposition Author(s): Kishor, C., Gumpena, R., Reddi, R., Addlagatta, A.

Revision History  

• Version 1.0: 2012-08-08
  Type: Initial release
  
• Version 1.1: 2013-06-26
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description