Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.05 kDa 
• Atom Count: 1054 
• Modelled Residue Count: 125 
• Deposited Residue Count: 125 
• Unique protein chains: 1

2QWS

Neutron and X-ray structural studies of short hydrogen bonds in Photoactive Yellow Protein (PYP)

• PDB DOI: 10.2210/pdb2QWS/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Halorhodospira halophila
• Mutation(s): No 


• Deposited: 2007-08-10 Released: 2008-03-18 
• Deposition Author(s): Fisher, S.Z., Langan, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.273 
• R-Value Work: 0.262 

Literature

Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP)

Fisher, S.Z., Anderson, S., Henning, R., Moffat, K., Langan, P., Thiyagarajan, P., Schultz, A.J.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1178-1184

• PubMed: 18007033 
• DOI: 10.1107/S0907444907047646
• Primary Citation of Related Structures:  
  2QWS


• PubMed Abstract: 
  

Photoactive yellow protein (PYP) from Halorhodospira halophila is a soluble 14 kDa blue-light photoreceptor. It absorbs light via its para-coumaric acid chromophore (pCA), which is covalently attached to Cys69 and is believed to be involved in the negative phototactic response of the organism to blue light. The complete structure (including H atoms) of PYP has been determined in D(2)O-soaked crystals through the application of joint X-ray (1.1 A) and neutron (2.5 A) structure refinement in combination with cross-validated maximum-likelihood simulated annealing. The resulting XN structure reveals that the phenolate O atom of pCA accepts deuterons from Glu46 O(epsilon2) and Tyr42 O(eta) in two unusually short hydrogen bonds. This arrangement is stabilized by the donation of a deuteron from Thr50 O(gamma1) to Tyr42 O(eta). However, the deuteron position between pCA and Tyr42 is only partially occupied. Thus, this atom may also interact with Thr50, possibly being disordered or fluctuating between the two bonds.

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Organizational Affiliation: 

Bioscience Division, Los Alamos National Laboratory, M888, Los Alamos, NM 87545, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photoactive yellow protein	A	125	Halorhodospira halophila	Mutation(s): 0  Gene Names: pyp
UniProt
Find proteins for P16113 (Halorhodospira halophila) Explore P16113  Go to UniProtKB:  P16113

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HC4	B [auth A]	4'-HYDROXYCINNAMIC ACID C9 H8 O3 NGSWKAQJJWESNS-ZZXKWVIFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.273 
• R-Value Work: 0.262 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.833	α = 90
b = 66.833	β = 90
c = 40.947	γ = 120

Software Package:

Software Name	Purpose
PCS	data collection
CNS	refinement
nCNS	refinement
d*TREK	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-08-10 
• Released Date: 2008-03-18 
Deposition Author(s): Fisher, S.Z., Langan, P.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-04-25
  Changes: Data collection