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- PDB-8aaq: Crystal structure of the carotenoid-binding protein domain from s... -

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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 / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.17 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

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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: 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

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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 °

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