Macromolecule Content

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

6Z3N

Apo Structure of a Hydrolase from Pseudomonas aeruginosa PAO1

PDB DOI: 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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.200
R-Value Work: 0.137

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Apo Structure of a Small Alarmone Hydrolase from Pseudomonas aeruginosa PAO1

Jin, Y., Rizkallah, P., Bell, H.

To be published.

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I686
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth CCC] MOL2 format, chain H [auth CCC]	H [auth CCC]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain I [auth CCC] MOL2 format, chain E [auth AAA] MOL2 format, chain I [auth CCC]	E [auth AAA], I [auth CCC]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain G [auth BBB] SDF format, chain J [auth CCC] SDF format, chain K [auth DDD] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth BBB] MOL2 format, chain J [auth CCC] MOL2 format, chain K [auth DDD]	F [auth AAA], G [auth BBB], J [auth CCC], K [auth DDD]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.137
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-06-09

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2021-06-09
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.