8E09 | pdb_00008e09

Crystal structure of photoactive yellow protein (PYP); F96oCNF M100E construct

• PDB DOI: https://doi.org/10.2210/pdb8E09/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Halorhodospira halophila
• Expression System: Escherichia coli str. K-12 substr. DH10B
• Mutation(s): Yes 


• Deposited: 2022-08-08 Released: 2022-08-24 
• Deposition Author(s): Kirsh, J.M., Weaver, J.B., Boxer, S.G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.01 Å
• R-Value Free: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Protic and Aprotic Interactions Systematically Perturbed and Mapped via MD and IR Spectroscopy

Kirsh, J.M., Kozuch, J., Weaver, J.B., Boxer, S.G.

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 Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 14.08 kDa 
• Atom Count: 1,277 
• Modeled Residue Count: 124 
• Deposited Residue Count: 125 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photoactive yellow protein	A	125	Halorhodospira halophila	Mutation(s): 1  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: 1.01 Å
• R-Value Free:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.206	α = 90
b = 66.206	β = 90
c = 40.608	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Kirsh, J.M., Weaver, J.B., Boxer, S.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	2R35GM11804406
National Science Foundation (NSF, United States)	United States	1915727

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection, Derived calculations