5OY5 | pdb_00005oy5

Monomeric crystal structure of RpBphP1 photosensory core domain from the bacterium Rhodopseudomonas palustris

• PDB DOI: https://doi.org/10.2210/pdb5OY5/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Rhodopseudomonas palustris CGA009
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-07 Released: 2019-02-06 
• Deposition Author(s): Papiz, M.Z., Bellini, D.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council, STFC Darebury Laboratory

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Insights into the light-induced molecular switch of the bacteriophytochrome RpBphP1 probed by SAXS, modelling and UV-Vis optical properties

Papiz, M.Z., Bellini, D.

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: gel filtration, native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 58.36 kDa 
• Atom Count: 4,057 
• Modeled Residue Count: 491 
• Deposited Residue Count: 525 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BphP1	A	525	Rhodopseudomonas palustris CGA009	Mutation(s): 0
UniProt
Find proteins for A0A161I5N6 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore A0A161I5N6  Go to UniProtKB:  A0A161I5N6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BLA	B [auth A]	BILIVERDINE IX ALPHA C33 H34 N4 O6 GWZYPXHJIZCRAJ-SRVCBVSDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.78	α = 90
b = 92.78	β = 90
c = 449.17	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Papiz, M.Z., Bellini, D.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/E002609/2
STFC Darebury Laboratory	United Kingdom	--

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary