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- PDB-7ztr: Crystal structure of the carotenoid-binding protein domain from s... -

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Basic information

Entry
Database: PDB / ID: 7ztr
TitleCrystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP) in the apoform, W232F mutant
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 / late endosome membrane / lysosomal membrane / lipid binding / 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 / molecular replacement / Resolution: 1.75 Å
AuthorsSluchanko, N.N. / Boyko, K.M. / Varfolomeeva, L.A. / Slonimskiy, Y.B. / Egorkin, N.A. / Maksimov, E.G. / Popov, V.O.
Funding support Russian Federation, Germany, 3items
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
German Research Foundation (DFG)FR1276/6-1 Germany
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Silkworm carotenoprotein as an efficient carotenoid extractor, solubilizer and transporter.
Authors: Sluchanko, N.N. / Slonimskiy, Y.B. / Egorkin, N.A. / Varfolomeeva, L.A. / Faletrov, Y.V. / Moysenovich, A.M. / Parshina, E.Y. / Friedrich, T. / Maksimov, E.G. / Boyko, K.M. / Popov, V.O.
History
DepositionMay 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carotenoid-binding protein


Theoretical massNumber of molelcules
Total (without water)28,4921
Polymers28,4921
Non-polymers00
Water3,225179
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 area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.033, 66.772, 120.502
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-335-

HOH

21A-431-

HOH

31A-445-

HOH

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Components

#1: Protein Carotenoid-binding protein


Mass: 28491.791 Da / Num. of mol.: 1 / Mutation: W232F
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.: 179 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.83 %
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

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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: Nov 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.75→60.25 Å / Num. obs: 25252 / % possible obs: 98.5 % / Redundancy: 11.5 % / CC1/2: 0.979 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.027 / Rrim(I) all: 0.09 / Net I/σ(I): 20.8 / Num. measured all: 289696 / Scaling rejects: 1127
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
1.75-1.784.80.848548011430.6090.4180.9521.884.8
9.09-60.255.60.04712122160.9940.0210.05239.598.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.7data scaling
MOLREPphasing
REFMAC5.8.0349refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZTQ

7ztq


Resolution: 1.75→60.25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.382 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 1209 4.8 %RANDOM
Rwork0.1811 ---
obs0.1836 24006 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.43 Å2 / Biso mean: 22.825 Å2 / Biso min: 11.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2---0.67 Å20 Å2
3---0.25 Å2
Refinement stepCycle: final / Resolution: 1.75→60.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 0 179 1996
Biso mean---31.63 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121878
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161741
X-RAY DIFFRACTIONr_angle_refined_deg2.0921.6412551
X-RAY DIFFRACTIONr_angle_other_deg0.8731.5484051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.545232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.5111016
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33410308
X-RAY DIFFRACTIONr_chiral_restr0.1370.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022145
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02379
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 69 -
Rwork0.25 1512 -
all-1581 -
obs--85.88 %
Refinement TLS params.Method: refined / Origin x: 15.8676 Å / Origin y: 12.7193 Å / Origin z: -17.1656 Å
111213212223313233
T0.0037 Å2-0.0064 Å20.0023 Å2-0.0268 Å20.0044 Å2--0.0073 Å2
L0.562 °2-0.1375 °20.2028 °2-1.6463 °20.0121 °2--1.2172 °2
S0.004 Å °-0.0321 Å °0.0049 Å °0.0504 Å °-0.025 Å °0.0885 Å °0.0289 Å °-0.0189 Å °0.021 Å °

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