3BYC | pdb_00003byc

Joint neutron and X-ray structure of diisopropyl fluorophosphatase. Deuterium occupancies are 1-Q, where Q is occupancy of H

• PDB DOI: https://doi.org/10.2210/pdb3BYC/pdb

• Classification: HYDROLASE
• Organism(s): Loligo vulgaris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-15 Released: 2009-01-27 
• Deposition Author(s): Blum, M.-M., Mustyakimov, M., Ruterjans, H., Schoenborn, B.P., Langan, P., Chen, J.C.-H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.252 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.213 (DCC) 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.315 (Depositor) 
• R-Value Work: 
  0.264 (Depositor) 

Literature

Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement.

Blum, M.M., Mustyakimov, M., Ruterjans, H., Kehe, K., Schoenborn, B.P., Langan, P., Chen, J.C.

(2009) Proc Natl Acad Sci U S A 106: 713-718

• PubMed: 19136630 
• DOI: https://doi.org/10.1073/pnas.0807842106
• Primary Citation Related Structures: 
  3BYC


• PubMed Abstract: 
  

  Hydrogen atoms constitute about half of all atoms in proteins and play a critical role in enzyme mechanisms and macromolecular and solvent structure. Hydrogen atom positions can readily be determined by neutron diffraction, and as such, neutron diffraction is an invaluable tool for elucidating molecular mechanisms. Joint refinement of neutron and X-ray diffraction data can lead to improved models compared with the use of neutron data alone and has now been incorporated into modern, maximum-likelihood based crystallographic refinement programs like CNS. Joint refinement has been applied to neutron and X-ray diffraction data collected on crystals of diisopropyl fluorophosphatase (DFPase), a calcium-dependent phosphotriesterase capable of detoxifying organophosphorus nerve agents. Neutron omit maps reveal a number of important features pertaining to the mechanism of DFPase. Solvent molecule W33, coordinating the catalytic calcium, is a water molecule in a strained coordination environment, and not a hydroxide. The smallest Ca-O-H angle is 53 degrees, well beyond the smallest angles previously observed. Residue Asp-229, is deprotonated, supporting a mechanism involving nucleophilic attack by Asp-229, and excluding water activation by the catalytic calcium. The extended network of hydrogen bonding interactions in the central water filled tunnel of DFPase is revealed, showing that internal solvent molecules form an important, integrated part of the overall structure.

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Organizational Affiliation: 
• Institute of Biophysical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany.

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: 35.2 kDa 
• Atom Count: 2,699 
• Modeled Residue Count: 312 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diisopropyl-fluorophosphatase	A	314	Loligo vulgaris	Mutation(s): 0  EC: 3.1.8.2 (PDB Primary Data), 3.8.2.2 (UniProt)
UniProt
Find proteins for Q7SIG4 (Loligo vulgaris) Explore Q7SIG4  Go to UniProtKB:  Q7SIG4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.252 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.213 (DCC) 

• Method: NEUTRON DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.315 (Depositor) 
• R-Value Work:  0.264 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.441	α = 90
b = 83.291	β = 90
c = 87.509	γ = 90

Software Package:

Software Name	Purpose
nCNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-27 
Deposition Author(s): Blum, M.-M., Mustyakimov, M., Ruterjans, H., Schoenborn, B.P., Langan, P., Chen, J.C.-H.

Revision History  

• Version 1.0: 2009-01-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Data collection, Non-polymer description, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations