9D2H | pdb_00009d2h

Stigmatella aurantica bacteriophytochrome protein 2 (SaBphP2), photosensory core module, investigated at ESRF(EBS) ID29. Dark Structure.

• PDB DOI: https://doi.org/10.2210/pdb9D2H/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Stigmatella aurantiaca
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.261 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.192 (Depositor) 
• R-Value Observed: 
  0.195 (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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 106.93 kDa 
• Atom Count: 7,806 
• Modeled Residue Count: 964 
• Deposited Residue Count: 980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
histidine kinase	A, B	490	Stigmatella aurantiaca	Mutation(s): 0  Gene Names: STIAU_8420 EC: 2.7.13.3
UniProt
Find proteins for Q09E27 (Stigmatella aurantiaca (strain DW4/3-1)) Explore Q09E27  Go to UniProtKB:  Q09E27

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BLA	C [auth A], E [auth B]	BILIVERDINE IX ALPHA C33 H34 N4 O6 GWZYPXHJIZCRAJ-SRVCBVSDSA-N
BEN	D [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.261 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.192 (Depositor) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.69	α = 90
b = 83.4	β = 107.63
c = 86.87	γ = 90

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): Schmidt, M., Malla, T.N.

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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