4JRR | pdb_00004jrr

Crystal structure of disulfide bond oxidoreductase DsbA1 from Legionella pneumophila

• PDB DOI: https://doi.org/10.2210/pdb4JRR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-21 Released: 2013-04-24 
• Deposition Author(s): Shumilin, I.A., Jameson-Lee, M., Cymborowski, M., Domagalski, M.J., Chertihin, O., Kpadeh, Z.Z., Yeh, A.J., Hoffman, P.S., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.205 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Crystal structure of disulfide bond oxidoreductase DsbA1 from Legionella pneumophila

Shumilin, I.A., Jameson-Lee, M., Cymborowski, M., Domagalski, M.J., Chertihin, O., Kpadeh, Z.Z., Yeh, A.J., Hoffman, P.S., Anderson, W.F., Minor, W.

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.

Macromolecule Content 

• Total Structure Weight: 65.05 kDa 
• Atom Count: 4,958 
• Modeled Residue Count: 557 
• Deposited Residue Count: 567 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol:disulfide interchange protein DsbA	A, B, C	189	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: dsbA, lpg0123
UniProt
Find proteins for Q5ZZ88 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZZ88  Go to UniProtKB:  Q5ZZ88

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], G [auth B], H [auth C], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], J [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.205 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m3qg6j

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.876	α = 90
b = 80.137	β = 92.86
c = 66.257	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-24 
Deposition Author(s): Shumilin, I.A., Jameson-Lee, M., Cymborowski, M., Domagalski, M.J., Chertihin, O., Kpadeh, Z.Z., Yeh, A.J., Hoffman, P.S., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Refinement description