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- PDB-8pre: The structure of nvBagel2 in the presence of Zn(II) -

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Basic information

Entry
Database: PDB / ID: 8pre
TitleThe structure of nvBagel2 in the presence of Zn(II)
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: 3.1 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

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Assembly

Deposited unit
A: Cell surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1823
Polymers9,0511
Non-polymers1312
Water543
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)36,72712
Polymers36,2044
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 area6020 Å2
ΔGint-35 kcal/mol
Surface area11670 Å2
Unit cell
Length a, b, c (Å)55.050, 55.050, 107.920
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

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Components

#1: Protein Cell surface protein


Mass: 9050.947 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.: 3 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.5
Details: 0.2 M Zinc acetate, 0.1 M Sodium cacodylate pH 6.5, 10% v/v Isopropanol

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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: 3.1→38.93 Å / Num. obs: 1682 / % possible obs: 100 % / Redundancy: 23.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.046 / Rrim(I) all: 0.218 / Net I/σ(I): 16.2 / Num. measured all: 40000
Reflection shellResolution: 3.1→3.15 Å / % possible obs: 100 % / Redundancy: 24.4 % / Rmerge(I) obs: 1.088 / Num. measured all: 1929 / Num. unique obs: 79 / CC1/2: 0.942 / Rpim(I) all: 0.223 / Rrim(I) all: 1.111 / Net I/σ(I) obs: 4.4

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
xia2data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→38.93 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 19.01 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2883 88 5.23 %
Rwork0.2291 --
obs0.2316 1681 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms603 0 2 3 608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002622
X-RAY DIFFRACTIONf_angle_d0.484845
X-RAY DIFFRACTIONf_dihedral_angle_d5.10284
X-RAY DIFFRACTIONf_chiral_restr0.04685
X-RAY DIFFRACTIONf_plane_restr0.003109
LS refinement shellResolution: 3.1→38.93 Å
RfactorNum. reflection% reflection
Rfree0.2883 88 -
Rwork0.2291 1593 -
obs--100 %

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