3JRU | pdb_00003jru

Crystal structure of Leucyl Aminopeptidase (pepA) from Xoo0834,Xanthomonas oryzae pv. oryzae KACC10331

• PDB DOI: https://doi.org/10.2210/pdb3JRU/pdb

• Classification: HYDROLASE
• Organism(s): Xanthomonas oryzae pv. oryzae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-08 Released: 2010-09-08 
• Deposition Author(s): Natarajan, S., Huynh, K.-H., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.215 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Leucyl Aminopeptidase (pepA) from Xoo0834,Xanthomonas oryzae pv. oryzae KACC10331

Natarajan, S., Huynh, K.-H., Kang, L.W.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 102.63 kDa 
• Atom Count: 7,884 
• Modeled Residue Count: 980 
• Deposited Residue Count: 980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable cytosol aminopeptidase	A [auth B], B [auth A]	490	Xanthomonas oryzae pv. oryzae	Mutation(s): 0  Gene Names: pepA, XOO0834 EC: 3.4.11.1 (PDB Primary Data), 3.4.11.10 (UniProt)
UniProt
Find proteins for Q5H4N2 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)) Explore Q5H4N2  Go to UniProtKB:  Q5H4N2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth B], E [auth B], H [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3	C [auth B], G [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
CA	F [auth B], J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.215 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.126	α = 90
b = 152.126	β = 90
c = 152.126	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Natarajan, S., Huynh, K.-H., Kang, L.W.

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description