8AAQ | pdb_00008aaq

Crystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP), CRT-416 form

• PDB DOI: https://doi.org/10.2210/pdb8AAQ/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bombyx mori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-01 Released: 2023-02-01 
• Deposition Author(s): Varfolomeeva, L.A., Slonimskiy, Y.B., Egorkin, N.A., Minyaev, M.E., Faletrov, Y.V., Boyko, K.M., Sluchanko, N.N.
• Funding Organization(s): Ministry of Science and Higher Education of the Russian Federation, Russian Foundation for Basic Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Preparation and Structural Studies of the Silkworm Carotenoid-Binding Protein Complexed with a New Pigment

Varfolomeeva, L.A., Slonimskiy, Y.B., Egorkin, N.A., Minyaev, M.E., Faletrov, Y.V., Boyko, K.M., Sluchanko, N.N.

(2022) Crystallogr Rep 

• DOI: https://doi.org/10.1134/S1063774522060281

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

Macromolecule Content 

• Total Structure Weight: 28.53 kDa 
• Atom Count: 2,003 
• Modeled Residue Count: 229 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carotenoid-binding protein	A	253	Bombyx mori	Mutation(s): 0  Gene Names: BmCBP
UniProt
Find proteins for Q8MYA9 (Bombyx mori) Explore Q8MYA9  Go to UniProtKB:  Q8MYA9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.119	α = 90
b = 66.445	β = 90
c = 120.262	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-01 
Deposition Author(s): Varfolomeeva, L.A., Slonimskiy, Y.B., Egorkin, N.A., Minyaev, M.E., Faletrov, Y.V., Boyko, K.M., Sluchanko, N.N.

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Funding Organization	Location	Grant Number
Ministry of Science and Higher Education of the Russian Federation	Russian Federation	075-15-2021-1354
Russian Foundation for Basic Research	Russian Federation	20-54-12018

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release
  
• Version 1.1: 2023-08-30
  Changes: Data collection, Database references
• Version 1.2: 2024-02-07
  Changes: Refinement description