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- PDB-8f0e: N-terminal WD40 domain of beta'-COPI subunit with four chains in ... -

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Basic information

Entry
Database: PDB / ID: 8f0e
TitleN-terminal WD40 domain of beta'-COPI subunit with four chains in the asymmetric unit
ComponentsCoatomer subunit beta'
KeywordsCYTOSOLIC PROTEIN / Retrograde trafficking / coatomer / COPI
Function / homology
Function and homology information


COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity
Similarity search - Function
Coatomer beta' subunit (COPB2) / Coatomer, WD associated region / : / : / COPA/B second beta-propeller / COPA/B TPR domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat ...Coatomer beta' subunit (COPB2) / Coatomer, WD associated region / : / : / COPA/B second beta-propeller / COPA/B TPR domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Coatomer subunit beta'
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsDey, D. / Hasan, S.S.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0012704 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA134274 United States
CitationJournal: Protein Expr.Purif. / Year: 2023
Title: Strategies for rapid production of crystallization quality coatomer WD40 domains.
Authors: Dey, D. / Hasan, S.S.
History
DepositionNov 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coatomer subunit beta'
B: Coatomer subunit beta'
C: Coatomer subunit beta'
D: Coatomer subunit beta'


Theoretical massNumber of molelcules
Total (without water)137,5234
Polymers137,5234
Non-polymers00
Water24,7171372
1
A: Coatomer subunit beta'


Theoretical massNumber of molelcules
Total (without water)34,3811
Polymers34,3811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Coatomer subunit beta'


Theoretical massNumber of molelcules
Total (without water)34,3811
Polymers34,3811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Coatomer subunit beta'


Theoretical massNumber of molelcules
Total (without water)34,3811
Polymers34,3811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Coatomer subunit beta'


Theoretical massNumber of molelcules
Total (without water)34,3811
Polymers34,3811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.115, 89.945, 138.324
Angle α, β, γ (deg.)90.000, 93.760, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Coatomer subunit beta'


Mass: 34380.730 Da / Num. of mol.: 4 / Fragment: N-terminal WD40 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: C8Z8B3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1372 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.31→29.37 Å / Num. obs: 286398 / % possible obs: 99.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 10.43 Å2 / CC1/2: 0.998 / Net I/σ(I): 6.5
Reflection shellResolution: 1.31→1.33 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 43255 / CC1/2: 0.653

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487+SVNrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8EWX

8ewx


Resolution: 1.31→29.13 Å / SU ML: 0.1268 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.7579
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1907 14259 4.99 %
Rwork0.1572 271558 -
obs0.1589 285817 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.31 Å2
Refinement stepCycle: LAST / Resolution: 1.31→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9550 0 0 1372 10922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089825
X-RAY DIFFRACTIONf_angle_d1.09613403
X-RAY DIFFRACTIONf_chiral_restr0.09531479
X-RAY DIFFRACTIONf_plane_restr0.01091696
X-RAY DIFFRACTIONf_dihedral_angle_d13.32353485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.320.30084160.25668697X-RAY DIFFRACTION94.8
1.32-1.340.28584330.23678869X-RAY DIFFRACTION98.16
1.34-1.360.27294600.21989038X-RAY DIFFRACTION98.92
1.36-1.370.24524740.21988960X-RAY DIFFRACTION99.62
1.37-1.390.23295050.20119061X-RAY DIFFRACTION99.96
1.39-1.410.24474880.19589047X-RAY DIFFRACTION99.87
1.41-1.430.23214740.1899005X-RAY DIFFRACTION99.92
1.43-1.450.23234510.18599136X-RAY DIFFRACTION99.87
1.45-1.480.22865240.18049011X-RAY DIFFRACTION99.91
1.48-1.50.2294880.17199046X-RAY DIFFRACTION99.86
1.5-1.530.21944870.16169050X-RAY DIFFRACTION99.85
1.53-1.550.1944860.14949047X-RAY DIFFRACTION99.93
1.55-1.580.19185170.14479060X-RAY DIFFRACTION99.91
1.58-1.620.18774780.1449023X-RAY DIFFRACTION99.86
1.62-1.650.20525250.14189017X-RAY DIFFRACTION99.86
1.65-1.690.1854730.14119061X-RAY DIFFRACTION99.88
1.69-1.730.18444620.1389106X-RAY DIFFRACTION99.85
1.73-1.780.18724560.14099059X-RAY DIFFRACTION99.85
1.78-1.830.20044450.14399136X-RAY DIFFRACTION99.79
1.83-1.890.17954530.1389092X-RAY DIFFRACTION99.82
1.89-1.960.17824970.13379055X-RAY DIFFRACTION99.81
1.96-2.040.17924480.13489092X-RAY DIFFRACTION99.77
2.04-2.130.16154850.13959068X-RAY DIFFRACTION99.7
2.13-2.240.15654590.14019128X-RAY DIFFRACTION99.82
2.24-2.380.16834540.13979062X-RAY DIFFRACTION99.77
2.38-2.560.17345150.14589118X-RAY DIFFRACTION99.91
2.56-2.820.18884400.15439109X-RAY DIFFRACTION99.77
2.82-3.230.19684510.16429156X-RAY DIFFRACTION99.76
3.23-4.070.1645190.15529130X-RAY DIFFRACTION99.8
4.07-29.130.19164960.17369119X-RAY DIFFRACTION98.41

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