4QAK | pdb_00004qak

Crystal structure of phosphoesterase

• PDB DOI: https://doi.org/10.2210/pdb4QAK/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2014-05-05 Released: 2014-10-22 
• Deposition Author(s): Remus, B.S., Shuman, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.229 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Structure of phosphoesterase

Remus, B.S., Shuman, S.

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: 41 kDa 
• Atom Count: 3,149 
• Modeled Residue Count: 345 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-5'-RNA ligase	A, B	177	Escherichia coli K-12	Mutation(s): 0  EC: 6.5.1 (PDB Primary Data), 3.1.4.58 (UniProt)
UniProt
Find proteins for P37025 (Escherichia coli (strain K12)) Explore P37025  Go to UniProtKB:  P37025

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2AM	F [auth B]	ADENOSINE-2'-MONOPHOSPHATE C10 H14 N5 O7 P QDFHPFSBQFLLSW-KQYNXXCUSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.229 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.688	α = 90
b = 107.688	β = 90
c = 71.657	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-22 
Deposition Author(s): Remus, B.S., Shuman, S.

Revision History  

• Version 1.0: 2014-10-22
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary