4Z42 | pdb_00004z42

Crystal structure of urease from Yersinia enterocolitica

• PDB DOI: https://doi.org/10.2210/pdb4Z42/pdb

• Classification: HYDROLASE
• Organism(s): Yersinia enterocolitica W22703
• Mutation(s): No 


• Deposited: 2015-04-01 Released: 2016-04-13 
• Deposition Author(s): Studer, G., Jakob, R.P., Mahi, M.A., Wiesand, U., Schwede, T., Maier, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 
  0.298 (Depositor), 0.356 (DCC) 
• R-Value Work: 
  0.277 (Depositor), 0.331 (DCC) 
• R-Value Observed: 
  0.278 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of urease from Yersinia enterocolitica

Studer, G., Jakob, R.P., Mahi, M.A., Wiesand, U., Schwede, T., Maier, T.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Hetero 36-mer - A12B12C12 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 361 kDa 
• Atom Count: 23,817 
• Modeled Residue Count: 3,136 
• Deposited Residue Count: 3,344 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease subunit gamma	A, D, G, J	100	Yersinia enterocolitica W22703	Mutation(s): 0  EC: 3.5.1.5
UniProt
Find proteins for F4MWM9 (Yersinia enterocolitica W22703) Explore F4MWM9  Go to UniProtKB:  F4MWM9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease subunit beta	B, E, H, K	164	Yersinia enterocolitica W22703	Mutation(s): 0  EC: 3.5.1.5
UniProt
Find proteins for F4MWM8 (Yersinia enterocolitica W22703) Explore F4MWM8  Go to UniProtKB:  F4MWM8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease subunit alpha	C, F, I, L	572	Yersinia enterocolitica W22703	Mutation(s): 0  EC: 3.5.1.5
UniProt
Find proteins for F4MWM7 (Yersinia enterocolitica W22703) Explore F4MWM7  Go to UniProtKB:  F4MWM7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	M [auth C], N [auth C], O [auth F], P [auth F], Q [auth I], R [auth I], S [auth L], T [auth L]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free:  0.298 (Depositor), 0.356 (DCC) 
• R-Value Work:  0.277 (Depositor), 0.331 (DCC) 
• R-Value Observed: 0.278 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.2	α = 90
b = 157.2	β = 90
c = 774.62	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Studer, G., Jakob, R.P., Mahi, M.A., Wiesand, U., Schwede, T., Maier, T.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2018-11-21
  Changes: Advisory, Data collection, Derived calculations
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description