[English] 日本語
Yorodumi
- PDB-8aaq: Crystal structure of the carotenoid-binding protein domain from s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8aaq
TitleCrystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP), CRT-416 form
ComponentsCarotenoid-binding protein
KeywordsTRANSPORT PROTEIN / carotenoid-binding protein / carotenoid transport / CBP / STARD / START domain / Bombyx mori
Function / homology
Function and homology information


vesicle tethering to endoplasmic reticulum / endoplasmic reticulum-endosome membrane contact site / cholesterol transport / cholesterol binding / late endosome membrane / lysosomal membrane / endoplasmic reticulum membrane
Similarity search - Function
in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START-like domain superfamily
Similarity search - Domain/homology
Carotenoid-binding protein
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVarfolomeeva, L.A. / Slonimskiy, Y.B. / Egorkin, N.A. / Minyaev, M.E. / Faletrov, Y.V. / Boyko, K.M. / Sluchanko, N.N.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
Russian Foundation for Basic Research20-54-12018 Russian Federation
CitationJournal: Crystallography Reports / Year: 2022
Title: Preparation and Structural Studies of the Silkworm Carotenoid-Binding Protein Complexed with a New Pigment
Authors: Varfolomeeva, L.A. / Slonimskiy, Y.B. / Egorkin, N.A. / Minyaev, M.E. / Faletrov, Y.V. / Boyko, K.M. / Sluchanko, N.N.
History
DepositionJul 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carotenoid-binding protein


Theoretical massNumber of molelcules
Total (without water)28,5311
Polymers28,5311
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.119, 66.445, 120.262
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

21A-431-

HOH

31A-441-

HOH

-
Components

#1: Protein Carotenoid-binding protein


Mass: 28530.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: BmCBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q8MYA9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.5 M Sodium citrate tribasic dihydrate, 0.1 M BIS-TRIS propane pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Feb 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.8→60.13 Å / Num. obs: 22589 / % possible obs: 96 % / Redundancy: 7.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.033 / Rrim(I) all: 0.09 / Net I/σ(I): 17.1 / Num. measured all: 170679 / Scaling rejects: 467
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.844.60.90944879810.5190.4511.0231.671.2
8.99-60.133.70.0277602030.9990.0150.03135.392.1

-
Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZTQ

7ztq


Resolution: 1.8→60.13 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.284 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 1104 4.9 %RANDOM
Rwork0.1925 ---
obs0.1944 21421 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.7 Å2 / Biso mean: 27.049 Å2 / Biso min: 13.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-0 Å2
2---0.45 Å20 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 1.8→60.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1814 0 0 162 1976
Biso mean---34.04 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0121855
X-RAY DIFFRACTIONr_angle_refined_deg2.5441.6382520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4965228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.54121.23797
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20415309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7121515
X-RAY DIFFRACTIONr_chiral_restr0.1690.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021406
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 51 -
Rwork0.311 1200 -
all-1251 -
obs--73.29 %
Refinement TLS params.Method: refined / Origin x: 16.0941 Å / Origin y: 12.7887 Å / Origin z: -17.2916 Å
111213212223313233
T0.0075 Å20.004 Å20.0067 Å2-0.0055 Å20.0034 Å2--0.0097 Å2
L0.4533 °2-0.0172 °20.1024 °2-0.8796 °2-0.0309 °2--0.8847 °2
S-0.0037 Å °-0.0364 Å °-0.0033 Å °0.0004 Å °-0.0057 Å °0.0493 Å °0.0278 Å °0.0219 Å °0.0095 Å °

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more