8QZY | pdb_00008qzy

Structural and biochemical characterization of diaminopimelate epimerase from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb8QZY/pdb

• Classification: ISOMERASE
• Organism(s): Pseudomonas aeruginosa PA14
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-10-30 Released: 2024-11-06 
• Deposition Author(s): Schneider, P., Blankenfeldt, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.177 (DCC) 

Starting Model: experimental

Literature

Structural and biochemical characterization of diaminopimelate epimerase from Pseudomonas aeruginosa

Schneider, P., Blankenfeldt, W.

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 and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 61.01 kDa 
• Atom Count: 4,636 
• Modeled Residue Count: 554 
• Deposited Residue Count: 556 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate epimerase	A, B	278	Pseudomonas aeruginosa PA14	Mutation(s): 0  Gene Names: dapF, PA14_69690 EC: 5.1.1.7
UniProt
Find proteins for Q51564 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q51564  Go to UniProtKB:  Q51564

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.177 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.542	α = 90
b = 88.58	β = 90
c = 97.128	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Schneider, P., Blankenfeldt, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release