4Y8E | pdb_00004y8e

PA3825-EAL Ca-Apo Structure

• PDB DOI: https://doi.org/10.2210/pdb4Y8E/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-02-16 Released: 2016-03-02 
• Deposition Author(s): Horrell, S., Bellini, D., Strange, R., Wagner, A., Walsh, M.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.223 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Structure of PA3825 from P. aeruginosa bound to cyclic di-GMP and pGpG: new insights for a potential three-metal catalytic mechanism of EAL domains

Bellini, D., Horrell, S., Strange, R., Wagner, A., Hitchin, A., Webb, J.S., Tews, I., Walch, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.49 kDa 
• Atom Count: 4,354 
• Modeled Residue Count: 508 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA3825 EAL	A, B	263	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA3825 EC: 3.1.4.52
UniProt
Find proteins for Q9HXH7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HXH7  Go to UniProtKB:  Q9HXH7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.223 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.44	α = 90
b = 59.82	β = 116.94
c = 96.69	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
MOLREP	phasing
xia2	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Horrell, S., Bellini, D., Strange, R., Wagner, A., Walsh, M.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 2.0: 2017-08-30
  Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description