4E3Y | pdb_00004e3y

X-ray structure of the Serratia marcescens endonuclease at 0.95 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4E3Y/pdb

• Classification: HYDROLASE
• Organism(s): Serratia marcescens
• Mutation(s): No 


• Deposited: 2012-03-11 Released: 2013-05-08 
• Deposition Author(s): Lashkov, A.A., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.145 (Depositor), 0.147 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.131 (DCC) 
• R-Value Observed: 
  0.131 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of the Serratia marcescens endonuclease at 0.95 A resolution

Lashkov, A.A., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 54.04 kDa 
• Atom Count: 4,617 
• Modeled Residue Count: 480 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease	A, B	245	Serratia marcescens	Mutation(s): 0  EC: 3.1.30.2
UniProt
Find proteins for P13717 (Serratia marcescens) Explore P13717  Go to UniProtKB:  P13717

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	D [auth A], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.145 (Depositor), 0.147 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.131 (DCC) 
• R-Value Observed: 0.131 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.265	α = 90
b = 73.418	β = 90
c = 67.924	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Lashkov, A.A., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary