9CGH | pdb_00009cgh

Photoactive yellow protein crystallized in situ on cyclic olefin copolymer microfluidic chip through counter diffusion

• PDB DOI: https://doi.org/10.2210/pdb9CGH/pdb

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


• Deposited: 2024-06-28 Released: 2025-06-04 
• Deposition Author(s): Liu, Z., Gu, K.K., Shelby, M.L., Roy, D., Muniyappan, S., Schmidt, M., Narayanasamy, S.R., Coleman, M.A., Frank, M., Kuhl, T.L.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.179 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Photoactive yellow protein crystallized in situ on cyclic olefin copolymer microfluidic chip through counter diffusion

Liu, Z., Gu, K.K., Shelby, M.L., Roy, D., Muniyappan, S., Schmidt, M., Narayanasamy, S.R., Coleman, M.A., Frank, M., Kuhl, T.L.

To be published.

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: 1,108 
• 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): 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: 1.32 Å
• R-Value Free:  0.179 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.194	α = 90
b = 41.194	β = 90
c = 117.819	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Liu, Z., Gu, K.K., Shelby, M.L., Roy, D., Muniyappan, S., Schmidt, M., Narayanasamy, S.R., Coleman, M.A., Frank, M., Kuhl, T.L.

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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	2153503
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM117342
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19 AI144184
Department of Energy (DOE, United States)	United States	P30GM133894

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release