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- PDB-8prj: The structure of v31Bagel8 -

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Basic information

Entry
Database: PDB / ID: 8prj
TitleThe structure of v31Bagel8
Componentsv31Bagel8
KeywordsBIOSYNTHETIC PROTEIN / Protein design / symmetric / assembly / self-assembly / beta-propeller
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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: v31Bagel8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5673
Polymers34,4961
Non-polymers712
Water10,917606
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-16 kcal/mol
Surface area12500 Å2
Unit cell
Length a, b, c (Å)94.254, 72.612, 55.904
Angle α, β, γ (deg.)90.00, 114.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-710-

HOH

21A-751-

HOH

31A-1100-

HOH

41A-1102-

HOH

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Components

#1: Protein v31Bagel8


Mass: 34495.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M TRIS pH 8.5, 8% (w/v) PEG 4000, 0.8 M Lithium chloride

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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: 1.4→51.02 Å / Num. obs: 67618 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.031 / Rrim(I) all: 0.082 / Χ2: 0.97 / Net I/σ(I): 13.4 / Num. measured all: 450665
Reflection shellResolution: 1.4→1.42 Å / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.411 / Num. measured all: 19576 / Num. unique obs: 3372 / CC1/2: 0.895 / Rpim(I) all: 0.185 / Rrim(I) all: 0.452 / Χ2: 0.93 / Net I/σ(I) obs: 3.4

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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: 1.4→51.02 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1673 3370 4.99 %
Rwork0.1352 --
obs0.1368 67591 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→51.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 2 606 3057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.841
X-RAY DIFFRACTIONf_dihedral_angle_d6.284400
X-RAY DIFFRACTIONf_chiral_restr0.082372
X-RAY DIFFRACTIONf_plane_restr0.007525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.24991540.18252674X-RAY DIFFRACTION100
1.42-1.440.2081300.16072673X-RAY DIFFRACTION100
1.44-1.460.19791320.15122662X-RAY DIFFRACTION100
1.46-1.490.19561450.13632687X-RAY DIFFRACTION100
1.49-1.510.21971360.13722642X-RAY DIFFRACTION100
1.51-1.540.17991220.12562689X-RAY DIFFRACTION100
1.54-1.570.16081290.12772682X-RAY DIFFRACTION100
1.57-1.60.1781510.12692667X-RAY DIFFRACTION100
1.6-1.640.21161380.12922646X-RAY DIFFRACTION100
1.64-1.680.15141340.11932668X-RAY DIFFRACTION100
1.68-1.720.16021470.12152654X-RAY DIFFRACTION100
1.72-1.760.16821300.12922688X-RAY DIFFRACTION100
1.76-1.820.18061380.13972672X-RAY DIFFRACTION100
1.82-1.870.17761580.13452649X-RAY DIFFRACTION100
1.87-1.940.17151630.12782645X-RAY DIFFRACTION100
1.94-2.020.16621610.12642653X-RAY DIFFRACTION100
2.02-2.110.15181490.12912670X-RAY DIFFRACTION100
2.11-2.220.16441320.1312692X-RAY DIFFRACTION100
2.22-2.360.14071370.13292675X-RAY DIFFRACTION100
2.36-2.540.16871340.1372692X-RAY DIFFRACTION100
2.54-2.80.18521340.14932700X-RAY DIFFRACTION100
2.8-3.20.18331430.14042678X-RAY DIFFRACTION100
3.21-4.040.14421330.12842720X-RAY DIFFRACTION100
4.04-51.020.14371400.1422743X-RAY DIFFRACTION100

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