6Z3N | pdb_00006z3n

Apo Structure of a Hydrolase from Pseudomonas aeruginosa PAO1

• PDB DOI: https://doi.org/10.2210/pdb6Z3N/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-05-21 Released: 2021-06-09 
• Deposition Author(s): Jin, Y., Rizkallah, P., Bell, H.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.140 (DCC) 

Literature

Apo Structure of a Small Alarmone Hydrolase from Pseudomonas aeruginosa PAO1

Jin, Y., Rizkallah, P., Bell, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 93.63 kDa 
• Atom Count: 6,228 
• Modeled Residue Count: 708 
• Deposited Residue Count: 820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrolase	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	205	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA0431
UniProt
Find proteins for Q9I686 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I686  Go to UniProtKB:  Q9I686

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H [auth CCC]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth AAA], I [auth CCC]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NI	F [auth AAA], G [auth BBB], J [auth CCC], K [auth DDD]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.140 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.31	α = 90
b = 85.9	β = 102.34
c = 122.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Jin, Y., Rizkallah, P., Bell, H.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	209057/Z/ 17/Z

Revision History  

• Version 1.0: 2021-06-09
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary