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

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Basic information

Entry
Database: PDB / ID: 8prm
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 / Outer membrane protein assembly factor BamB / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2205
Polymers36,2044
Non-polymers12,0161
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.540, 79.818, 123.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Cell surface protein


Mass: 9050.947 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / 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.: 4 / 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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8
Details: 0.1 M Tris pH 8.5, 5% (w/v) PEG 6000 (final pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 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: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.2→46.11 Å / Num. obs: 30774 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.048 / Rrim(I) all: 0.164 / Χ2: 0.95 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.837 / Num. measured all: 18768 / Num. unique obs: 1382 / CC1/2: 0.951 / Rpim(I) all: 0.236 / Rrim(I) all: 0.87 / Χ2: 0.76 / Net I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.91 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 1458 4.74 %
Rwork0.1986 --
obs0.2016 30774 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 240 4 2656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022808
X-RAY DIFFRACTIONf_angle_d0.6244300
X-RAY DIFFRACTIONf_dihedral_angle_d4.183592
X-RAY DIFFRACTIONf_chiral_restr0.051356
X-RAY DIFFRACTIONf_plane_restr0.004436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.37521380.28112921X-RAY DIFFRACTION100
2.28-2.370.32281260.2672947X-RAY DIFFRACTION100
2.37-2.480.29841500.26232920X-RAY DIFFRACTION100
2.48-2.610.32581590.27022909X-RAY DIFFRACTION100
2.61-2.770.34721410.2432973X-RAY DIFFRACTION100
2.77-2.990.27981080.24822966X-RAY DIFFRACTION100
2.99-3.290.25771510.21662910X-RAY DIFFRACTION100
3.29-3.760.26541760.20882911X-RAY DIFFRACTION100
3.76-4.730.29861600.16592922X-RAY DIFFRACTION100
4.74-39.910.17121490.13492937X-RAY DIFFRACTION100

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