5CU1 | pdb_00005cu1

Crystal structure of DMSP lyase DddQ from Ruegeria pomeroyi DSS-3

• PDB DOI: https://doi.org/10.2210/pdb5CU1/pdb

• Classification: LYASE
• Organism(s): Ruegeria pomeroyi DSS-3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-24 Released: 2016-08-17 
• Deposition Author(s): Chong, S.Y., Moran, M.A., Lanzilotta, W.N., Whitman, W.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.267 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

To be Published

Chong, S.Y., Lanzilotta, W.N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.42 kDa 
• Atom Count: 1,590 
• Modeled Residue Count: 197 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DMSP lyase	A	212	Ruegeria pomeroyi DSS-3	Mutation(s): 0  Gene Names: dddQ, SPO1596 EC: 4.4.1.3
UniProt
Find proteins for Q5LT18 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LT18  Go to UniProtKB:  Q5LT18

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.267 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.582	α = 90
b = 69.878	β = 90
c = 49.731	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-2000	data scaling
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): Chong, S.Y., Moran, M.A., Lanzilotta, W.N., Whitman, W.B.

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description