9D10 | pdb_00009d10

Photoactive Yellow Protein, crystals from PEG, room temperature

• PDB DOI: https://doi.org/10.2210/pdb9D10/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Halorhodospira halophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-07 Released: 2025-01-15 
• Deposition Author(s): Malla, T.N., Schmidt, M.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Exploiting fourth-generation synchrotron radiation for enzyme and photoreceptor characterization.

Malla, T.N., Muniyappan, S., Menendez, D., Ogukwe, F., Dale, A.N., Clayton, J.D., Weatherall, D.D., Karki, P., Dangi, S., Mandella, V., Pacheco, A.A., Stojkovic, E.A., Rose, S.L., Orlans, J., Basu, S., de Sanctis, D., Schmidt, M.

(2025) IUCrJ 12: 36-48

• PubMed: 39575537 
• DOI: https://doi.org/10.1107/S2052252524010868
• Primary Citation Related Structures: 
  9CUF, 9D10, 9D2H


• PubMed Abstract: 
  

  The upgrade of the European Synchrotron Radiation Facility (ESRF) in Grenoble, France to an Extremely Brilliant Source (EBS) is expected to enable time-resolved synchrotron serial crystallography (SSX) experiments with sub-millisecond time resolution. ID29 is a new beamline dedicated to SSX experiments at ESRF-EBS. Here, we report experiments emerging from the initial phase of user operation at ID29. We first used microcrystals of photoactive yellow protein as a model system to exploit the potential of microsecond pulses for SSX. Subsequently, we investigated microcrystals of cytochrome c nitrite reductase (ccNiR) with microsecond X-ray pulses. CcNiR is a decaheme protein that is ideal for the investigation of radiation damage at the various heme-iron sites. Finally, we performed a proof-of-concept subsecond time-resolved SSX experiment by photoactivating microcrystals of a myxobacterial phytochrome.

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Organizational Affiliation: 
• Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, USA.
Department of Biology, Northeastern Illinois University, Chicago, USA.
Department of Chemistry, University of Wisconsin-Milwaukee, Milwaukee, USA.
European Synchrotron Radiation Facility (ESRF), Grenoble, France.
European Molecular Biology Laboratory (EMBL), Grenoble, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.05 kDa 
• Atom Count: 1,066 
• Modeled Residue Count: 125 
• 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): 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 (Subject of Investigation/LOI)	B [auth A]	4'-HYDROXYCINNAMIC ACID C9 H8 O3 NGSWKAQJJWESNS-ZZXKWVIFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.36	α = 90
b = 41.36	β = 90
c = 118.87	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Malla, T.N., Schmidt, M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1231306
National Science Foundation (NSF, United States)	United States	2423601

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Database references