8BCI | pdb_00008bci

Crystal structure of short-chain dehydrogenase PA3128 from Pseudomonas aeruginosa PAO1

• PDB DOI: https://doi.org/10.2210/pdb8BCI/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-16 Released: 2022-11-30 
• Deposition Author(s): Popp, M.A., Vit, A., Blankenfeldt, W.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.186 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

The structure of short-chain dehydrogenase PA3128 from Pseudomonas aeruginosa PAO1

Popp, M.A., Vit, A., 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.

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: 107.05 kDa 
• Atom Count: 8,058 
• Modeled Residue Count: 952 
• Deposited Residue Count: 1,000 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable short-chain dehydrogenase	A, B, C, D	250	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA3128
UniProt
Find proteins for Q9HZ96 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HZ96  Go to UniProtKB:  Q9HZ96

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	E [auth A], F [auth B], G [auth B], I [auth C], J [auth C], K [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	H [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.186 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 221.335	α = 90
b = 65.688	β = 107.35
c = 66.269	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-30 
Deposition Author(s): Popp, M.A., Vit, A., Blankenfeldt, W.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	BL587/5-1

Revision History  

• Version 1.0: 2022-11-30
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description