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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.231 (Depositor), 0.210 (DCC)
R-Value Work:
0.193 (Depositor)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

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

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8MYA9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.231 (Depositor), 0.210 (DCC)
R-Value Work: 0.193 (Depositor)
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

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-01

Deposition Author(s):

Varfolomeeva, L.A.

Slonimskiy, Y.B.

Sluchanko, N.N.

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.