1Y7E | pdb_00001y7e

The Crystal Structure of Aminopeptidase I from Borrelia burgdorferi B31

• PDB DOI: https://doi.org/10.2210/pdb1Y7E/pdb

• Classification: HYDROLASE
• Organism(s): Borreliella burgdorferi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-12-08 Released: 2005-01-04 
• Deposition Author(s): Min, T., Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.258 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

The crystal structure of aminopeptidase I (yscI) from Borrelia burgdorferi

Min, T., Gorman, J., Shapiro, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 51.89 kDa 
• Atom Count: 3,296 
• Modeled Residue Count: 404 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable M18-family aminopeptidase 1	A	458	Borreliella burgdorferi	Mutation(s): 7  Gene Names: apeA EC: 3.4.11
UniProt
Find proteins for P0C925 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31)) Explore P0C925  Go to UniProtKB:  P0C925

Small Molecules

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: 3.20 Å
• R-Value Free:  0.258 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 244.271	α = 90
b = 244.271	β = 90
c = 244.271	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-04 
Deposition Author(s): Min, T., Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-01-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary