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- PDB-8prl: The structure of v22Bagel8 -

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Basic information

Entry
Database: PDB / ID: 8prl
TitleThe structure of v22Bagel8
ComponentsCell surface protein
KeywordsBIOSYNTHETIC PROTEIN / Protein design / symmetric / assembly / self-assembly / beta-propeller
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process
Similarity search - Function
: / PQQ-like domain / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Cell surface protein
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsVandebroek, L. / Voet, A.R.D. / Lee, X.Y.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1235722N Belgium
CitationJournal: To Be Published
Title: The structure of v13Bagel8
Authors: Vandebroek, L. / Voet, A.R.D. / Lee, X.Y.
History
DepositionJul 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell surface protein
B: Cell surface protein


Theoretical massNumber of molelcules
Total (without water)17,5372
Polymers17,5372
Non-polymers00
Water46826
1
A: Cell surface protein

A: Cell surface protein

B: Cell surface protein

B: Cell surface protein


Theoretical massNumber of molelcules
Total (without water)35,0754
Polymers35,0754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation5_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation6_455x-1/2,-y+1/2,-z+1/21
Buried area7130 Å2
ΔGint-39 kcal/mol
Surface area12720 Å2
Unit cell
Length a, b, c (Å)56.447, 56.447, 113.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-111-

HOH

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Components

#1: Protein Cell surface protein


Mass: 8768.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: DICTH_0179
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B5YBJ6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 5
Details: 0.1 M Citric acid pH 4.0, 20% (w/v) PEG 6000 (final pH 5.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.65→28.26 Å / Num. obs: 5777 / % possible obs: 99.8 % / Redundancy: 22.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.044 / Rrim(I) all: 0.213 / Χ2: 1.02 / Net I/σ(I): 10.4 / Num. measured all: 131850
Reflection shellResolution: 2.65→2.78 Å / % possible obs: 99.2 % / Redundancy: 17.8 % / Rmerge(I) obs: 0.814 / Num. measured all: 13067 / Num. unique obs: 733 / CC1/2: 0.922 / Rpim(I) all: 0.188 / Rrim(I) all: 0.837 / Χ2: 0.83 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→28.26 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3702 300 5.24 %
Rwork0.2834 --
obs0.2879 5727 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→28.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 0 26 1266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091278
X-RAY DIFFRACTIONf_angle_d1.0071734
X-RAY DIFFRACTIONf_dihedral_angle_d7.342172
X-RAY DIFFRACTIONf_chiral_restr0.058174
X-RAY DIFFRACTIONf_plane_restr0.007224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-3.340.41481550.27012624X-RAY DIFFRACTION99
3.34-28.260.34831450.28922803X-RAY DIFFRACTION100

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