5C31

Constitutively active Sin recombinase catalytic domain reveals two rotational intermediates

• PDB DOI: https://doi.org/10.2210/pdb5C31/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-06-16 Released: 2016-12-21 
• Deposition Author(s): Trejo, C.S., Rice, P.A.
• Funding Organization(s): National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.286 
• R-Value Work: 0.227 
• R-Value Observed: 0.230 

Literature

Snapshots of a molecular swivel in action

Trejo, C.S., Rock, R.S., Star, W.M., Boocock, M.R., Rice, P.A.

(2018) Nucleic Acids Res 

• DOI: https://doi.org/10.1093/nar/gkx1309

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 183.83 kDa 
• Atom Count: 12,305 
• Modelled Residue Count: 1,501 
• Deposited Residue Count: 1,536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sin, putative plasmid resolvase dimer	A, B, C, D, E, F, G, H, I, J, K, L	128	Staphylococcus aureus	Mutation(s): 2  Gene Names: Sin
UniProt
Find proteins for P20384 (Staphylococcus aureus) Explore P20384  Go to UniProtKB:  P20384

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth I], BA [auth I], CA [auth J], DA [auth J], EA [auth K], FA [auth L], GA [auth L], M [auth A], N [auth B], O [auth B], P [auth C], Q [auth C], R [auth D], S [auth E], T [auth F], U [auth G], V [auth H], W [auth H], X [auth H], Y [auth I], Z [auth I]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.286 
• R-Value Work: 0.227 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.15785/SBGRID/146

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.589	α = 90
b = 152.719	β = 90
c = 193.753	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Trejo, C.S., Rice, P.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)	United States	T32EB009412
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM086826
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM078450

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence
• Version 1.2: 2018-01-17
  Changes: Database references
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection