[English] 日本語
Yorodumi
- PDB-9ink: Crystal structure of beta-carotene-binding protein (BBP) from Sch... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ink
TitleCrystal structure of beta-carotene-binding protein (BBP) from Schistocerca gregaria complexed with beta-carotene
ComponentsYellow protein of the takeout family
KeywordsLIPID BINDING PROTEIN / Complex with beta-carotene / carotenoprotein / takeout-1 domain / tubular lipid-binding protein (TULIPs) / carotenoid solubilizer / dimer
Function / homologyHaemolymph juvenile hormone binding / Takeout superfamily / Haemolymph juvenile hormone binding protein (JHBP) / Juvenile hormone binding protein domains in insects. / extracellular space / BETA-CAROTENE / Yellow protein of the takeout family
Function and homology information
Biological speciesSchistocerca gregaria (desert locust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBoyko, K.M. / Varfolomeeva, L.A. / Egorkin, N.A. / Popov, V.O. / Sluchanko, N.N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Structural basis of selective beta-carotene binding by a soluble protein.
Authors: Egorkin, N.A. / Dominnik, E.E. / Raevskii, R.I. / Kuklina, D.D. / Varfolomeeva, L.A. / Popov, V.O. / Boyko, K.M. / Sluchanko, N.N.
History
DepositionJul 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Yellow protein of the takeout family
B: Yellow protein of the takeout family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5534
Polymers52,4802
Non-polymers1,0742
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-41 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.390, 75.510, 224.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Yellow protein of the takeout family / Tubular lipid-binding protein


Mass: 26239.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistocerca gregaria (desert locust) / Gene: YPT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A6N3ISN1
#2: Chemical ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Potassium acetate, pH 4.0, 0.2 M Potassium chloride, 20% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→28.88 Å / Num. obs: 13341 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.981 / Rmerge(I) obs: 0.411 / Rpim(I) all: 0.171 / Rrim(I) all: 0.446 / Χ2: 1.02 / Net I/σ(I): 4.4 / Num. measured all: 89039
Reflection shellResolution: 2.7→2.83 Å / % possible obs: 99.6 % / Redundancy: 6.8 % / Rmerge(I) obs: 2.85 / Num. measured all: 11717 / Num. unique obs: 1729 / CC1/2: 0.31 / Rpim(I) all: 1.178 / Rrim(I) all: 3.089 / Χ2: 0.95 / Net I/σ(I) obs: 0.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→28.88 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.898 / SU B: 56.162 / SU ML: 0.448 / Cross valid method: THROUGHOUT / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27766 653 4.9 %RANDOM
Rwork0.22119 ---
obs0.22412 12653 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.77 Å20 Å2
3---0.37 Å2
Refinement stepCycle: 1 / Resolution: 2.7→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3189 0 80 5 3274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123339
X-RAY DIFFRACTIONr_bond_other_d0.0040.0163202
X-RAY DIFFRACTIONr_angle_refined_deg2.3131.7864580
X-RAY DIFFRACTIONr_angle_other_deg1.0621.7037386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.345439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.7410474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1280.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023973
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02695
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1723.5881762
X-RAY DIFFRACTIONr_mcbond_other4.1693.5891762
X-RAY DIFFRACTIONr_mcangle_it6.3326.4882199
X-RAY DIFFRACTIONr_mcangle_other6.3326.4882200
X-RAY DIFFRACTIONr_scbond_it4.4523.8451577
X-RAY DIFFRACTIONr_scbond_other4.4513.8451578
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8976.9882382
X-RAY DIFFRACTIONr_long_range_B_refined9.4752.447429
X-RAY DIFFRACTIONr_long_range_B_other9.4752.447430
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 42 -
Rwork0.381 946 -
obs--99.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5703-0.33780.13482.9792-1.02070.83520.15430.06980.00750.0088-0.2486-0.1709-0.17860.07430.09430.2509-0.0791-0.03820.15380.04380.0204-0.252329.074118.6524
21.05680.4741-0.54381.542-1.15221.9013-0.0599-0.2041-0.0875-0.0801-0.0196-0.04950.10610.17310.07950.1579-0.068-0.00970.17550.00460.0173-7.9392-30.452641.4534
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 301
2X-RAY DIFFRACTION2B26 - 301

+
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://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