7Y1S | pdb_00007y1s

Crystal structure of apo leucyl aminopeptidase from Bacillus amyloliquefaciens

• PDB DOI: https://doi.org/10.2210/pdb7Y1S/pdb

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


• Deposited: 2022-06-08 Released: 2023-07-05 
• Deposition Author(s): Huang, P., Jiang, Z.Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 

Starting Model: experimental

Literature

Crystal structure of apo leucyl aminopeptidase from Bacillus amyloliquefaciens

Huang, P., Jiang, Z.Q.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 56.09 kDa 
• Atom Count: 3,763 
• Modeled Residue Count: 494 
• Deposited Residue Count: 519 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
leucyl aminopeptidase	A	519	Bacillus amyloliquefaciens	Mutation(s): 0  EC: 3.4.11.1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3 (Subject of Investigation/LOI)	B [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
NI (Subject of Investigation/LOI)	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.245	α = 90
b = 200.245	β = 90
c = 89.022	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Huang, P., Jiang, Z.Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description