1EJX | pdb_00001ejx

CRYSTAL STRUCTURE OF WILD-TYPE KLEBSIELLA AEROGENES UREASE AT 100K

• PDB DOI: https://doi.org/10.2210/pdb1EJX/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella aerogenes
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-03-04 Released: 2003-07-08 
• Deposition Author(s): Pearson, M.A., Karplus, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.240 (Depositor) 
• R-Value Work: 
  0.172 (Depositor), 0.171 (DCC) 

Literature

Crystal Structure of Wild-type Klebsiella aerogenes Urease at 100K

Pearson, M.A., Karplus, P.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 

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

Macromolecule Content 

• Total Structure Weight: 82.75 kDa 
• Atom Count: 6,272 
• Modeled Residue Count: 757 
• Deposited Residue Count: 768 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UREASE ALPHA SUBUNIT	A [auth C]	567	Klebsiella aerogenes	Mutation(s): 1  EC: 3.5.1.5
UniProt
Find proteins for P18314 (Klebsiella aerogenes) Explore P18314  Go to UniProtKB:  P18314

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UREASE BETA SUBUNIT	B	101	Klebsiella aerogenes	Mutation(s): 0  EC: 3.5.1.5
UniProt
Find proteins for P18315 (Klebsiella aerogenes) Explore P18315  Go to UniProtKB:  P18315

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
UREASE GAMMA SUBUNIT	C [auth A]	100	Klebsiella aerogenes	Mutation(s): 0  EC: 3.5.1.5
UniProt
Find proteins for P18316 (Klebsiella aerogenes) Explore P18316  Go to UniProtKB:  P18316

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	D [auth C], E [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A [auth C]	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.240 (Depositor) 
• R-Value Work:  0.172 (Depositor), 0.171 (DCC) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.96	α = 90
b = 168.96	β = 90
c = 168.96	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-08 
Deposition Author(s): Pearson, M.A., Karplus, P.A.

Revision History  

• Version 1.0: 2003-07-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary