2ZPL | pdb_00002zpl

Crystal structure analysis of PDZ domain A

• PDB DOI: https://doi.org/10.2210/pdb2ZPL/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-07-17 Released: 2008-10-21 
• Deposition Author(s): Inaba, K., Suzuki, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.175 (Depositor) 
• R-Value Work: 
  0.150 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

Crystal structure analysis of PDZ-domain A

Inaba, K., Suzuki, M., Maegawa, K., Akiyama, Y.

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.92 kDa 
• Atom Count: 2,244 
• Modeled Residue Count: 275 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulator of sigma E protease	A, B, C	97	Escherichia coli K-12	Mutation(s): 1  EC: 3.4.24
UniProt
Find proteins for P0AEH1 (Escherichia coli (strain K12)) Explore P0AEH1  Go to UniProtKB:  P0AEH1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth B], H [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	D [auth A], E [auth B], G [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.175 (Depositor) 
• R-Value Work:  0.150 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.756	α = 90
b = 54.756	β = 90
c = 75.644	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
and	data scaling
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-21 
Deposition Author(s): Inaba, K., Suzuki, M.

Revision History  

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary