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- PDB-8prb: The structure of v13Bagel6 -

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Basic information

Entry
Database: PDB / ID: 8prb
TitleThe structure of v13Bagel6
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: 1.8 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 v13Bagel6
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

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Assembly

Deposited unit
A: Cell surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2393
Polymers9,1081
Non-polymers1312
Water79344
1
A: Cell surface protein
hetero molecules

A: Cell surface protein
hetero molecules

A: Cell surface protein
hetero molecules

A: Cell surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,95512
Polymers36,4324
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area8380 Å2
ΔGint-44 kcal/mol
Surface area11900 Å2
Unit cell
Length a, b, c (Å)54.633, 54.633, 109.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-101-

ZN

21A-102-

ZN

31A-224-

HOH

41A-225-

HOH

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Components

#1: Protein Cell surface protein


Mass: 9107.999 Da / Num. of mol.: 1
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.5
Details: 0.0085 M Zinc sulfate, 0.085 M MES pH 6.5, 21.25 %(w/v) PEG 550 MME, 15 %(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→48.86 Å / Num. obs: 8033 / % possible obs: 100 % / Redundancy: 24 % / CC1/2: 1 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.024 / Rrim(I) all: 0.12 / Χ2: 0.93 / Net I/σ(I): 18.2 / Num. measured all: 192701
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 100 % / Redundancy: 25.1 % / Rmerge(I) obs: 1.165 / Num. measured all: 11334 / Num. unique obs: 451 / CC1/2: 0.972 / Rpim(I) all: 0.236 / Rrim(I) all: 1.189 / Χ2: 0.98 / Net I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.63 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 29.01 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2293 393 4.89 %
Rwork0.2125 --
obs0.2133 8030 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms612 0 2 44 658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008655
X-RAY DIFFRACTIONf_angle_d0.968893
X-RAY DIFFRACTIONf_dihedral_angle_d6.29189
X-RAY DIFFRACTIONf_chiral_restr0.07188
X-RAY DIFFRACTIONf_plane_restr0.008117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-2.060.26291220.20442473X-RAY DIFFRACTION100
2.06-2.60.26441360.21022516X-RAY DIFFRACTION100
2.6-38.630.21381350.21492648X-RAY DIFFRACTION100

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