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- PDB-8pro: The structure of nvBagel2 binding the P8W48O184 polyoxometalate -

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Basic information

Entry
Database: PDB / ID: 8pro
TitleThe structure of nvBagel2 binding the P8W48O184 polyoxometalate
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 speciesDictyoglomus thermophilum H-6-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)20,6532
Polymers8,6371
Non-polymers12,0161
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)82,6148
Polymers34,5504
Non-polymers48,0644
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
Unit cell
Length a, b, c (Å)54.848, 54.848, 118.430
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-201-

HOH

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Components

#1: Protein Cell surface protein


Mass: 8637.474 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyoglomus thermophilum H-6-12 (bacteria)
Strain: ATCC 35947 / DSM 3960 / H-6-12 / Gene: DICTH_0179
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B5YBJ6
#2: Chemical ChemComp-IR0 / P8W48O184 polyoxometalate


Mass: 12016.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O184P8W48 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 4.6 / Details: 0.1 M Sodium acetate pH 4.6, 15% (w/v) PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972423 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972423 Å / Relative weight: 1
ReflectionResolution: 1.7→38.78 Å / Num. obs: 18885 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.054 / Rrim(I) all: 0.136 / Χ2: 0.96 / Net I/σ(I): 11.7
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.806 / Num. measured all: 3383 / Num. unique obs: 525 / CC1/2: 0.954 / Rpim(I) all: 0.345 / Rrim(I) all: 0.878 / Χ2: 0.96 / Net I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→38.78 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 943 4.99 %
Rwork0.1647 --
obs0.1655 18885 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms612 0 240 44 896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091311
X-RAY DIFFRACTIONf_angle_d1.5132758
X-RAY DIFFRACTIONf_dihedral_angle_d5.365605
X-RAY DIFFRACTIONf_chiral_restr0.079122
X-RAY DIFFRACTIONf_plane_restr0.007122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.790.27571370.23782556X-RAY DIFFRACTION99
1.79-1.90.2911130.21122582X-RAY DIFFRACTION99
1.9-2.050.21171410.18962552X-RAY DIFFRACTION99
2.05-2.250.19871530.18082544X-RAY DIFFRACTION100
2.25-2.580.16421330.16382569X-RAY DIFFRACTION100
2.58-3.250.18841210.14782588X-RAY DIFFRACTION99
3.25-38.780.14721450.14442551X-RAY DIFFRACTION99

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