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- PDB-8pr9: The structure of v13Bagel2 -

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Basic information

Entry
Database: PDB / ID: 8pr9
TitleThe structure of v13Bagel2
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 / metal ion binding
Similarity search - Function
: / Beta-alanine-activating enzyme, beta-propeller / Pyrrolo-quinoline quinone repeat / 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: 2.35 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 v13Bagel2
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
C: Cell surface protein
D: Cell surface protein
E: Cell surface protein
F: Cell surface protein
G: Cell surface protein
H: Cell surface protein


Theoretical massNumber of molelcules
Total (without water)72,8648
Polymers72,8648
Non-polymers00
Water1,31573
1
A: Cell surface protein
D: Cell surface protein
F: Cell surface protein
G: Cell surface protein


Theoretical massNumber of molelcules
Total (without water)36,4324
Polymers36,4324
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-45 kcal/mol
Surface area12250 Å2
2
B: Cell surface protein
C: Cell surface protein
E: Cell surface protein
H: Cell surface protein


Theoretical massNumber of molelcules
Total (without water)36,4324
Polymers36,4324
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-44 kcal/mol
Surface area12300 Å2
Unit cell
Length a, b, c (Å)74.518, 83.515, 96.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Cell surface protein


Mass: 9107.999 Da / Num. of mol.: 8
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.: 73 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7 / Details: 0.1 M HEPES pH 7 30% v/v Jeffamine M-600 pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.35→96.95 Å / Num. obs: 25904 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.035 / Rrim(I) all: 0.127 / Net I/σ(I): 8.4 / Num. measured all: 331634
Reflection shellResolution: 2.35→2.39 Å / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.816 / Num. measured all: 14219 / Num. unique obs: 1272 / CC1/2: 0.952 / Rpim(I) all: 0.254 / Rrim(I) all: 0.856 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
xia2data scaling
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→63.35 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 13.813 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R: 0.583 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29406 1264 4.9 %RANDOM
Rwork0.23644 ---
obs0.23937 24585 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.71 Å20 Å2-0 Å2
2---3.83 Å20 Å2
3---1.12 Å2
Refinement stepCycle: 1 / Resolution: 2.35→63.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4904 0 0 73 4977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0125056
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164320
X-RAY DIFFRACTIONr_angle_refined_deg2.3481.656872
X-RAY DIFFRACTIONr_angle_other_deg0.741.58210112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6635632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25110736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021032
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.5834.1282552
X-RAY DIFFRACTIONr_mcbond_other7.5834.1282552
X-RAY DIFFRACTIONr_mcangle_it9.8826.1733176
X-RAY DIFFRACTIONr_mcangle_other9.886.1753177
X-RAY DIFFRACTIONr_scbond_it9.8484.8742504
X-RAY DIFFRACTIONr_scbond_other9.8474.8752505
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.0196.9973697
X-RAY DIFFRACTIONr_long_range_B_refined14.66456.3265521
X-RAY DIFFRACTIONr_long_range_B_other14.66756.3365522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 79 -
Rwork0.39 1795 -
obs--100 %

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