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- PDB-8prd: The structure of nvBagel2 -

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Basic information

Entry
Database: PDB / ID: 8prd
TitleThe structure of nvBagel2
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
Similarity search - Function
: / PQQ-like domain / Pyrrolo-quinoline quinone repeat / PQQ-like domain / 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: 1.41 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


Theoretical massNumber of molelcules
Total (without water)9,0511
Polymers9,0511
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.490, 62.490, 36.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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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.) Dictyoglomus thermophilum (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.96 Å3/Da / Density % sol: 37.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7.5
Details: 0.09 M HEPES sodium salt pH 7.5, 1.26 M tri-Sodium citrate, 10 %(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.4→44.19 Å / Num. obs: 12002 / % possible obs: 86.2 % / Redundancy: 10.2 % / CC1/2: 1 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.009 / Rrim(I) all: 0.033 / Χ2: 0.87 / Net I/σ(I): 30.2 / Num. measured all: 122125
Reflection shellResolution: 1.4→1.44 Å / % possible obs: 30 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.638 / Num. measured all: 525 / Num. unique obs: 301 / CC1/2: 0.698 / Rpim(I) all: 0.579 / Rrim(I) all: 0.866 / Χ2: 0.69 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→44.19 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 38.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 571 4.77 %
Rwork0.1783 --
obs0.1813 11969 87.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.41→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms604 0 0 34 638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012637
X-RAY DIFFRACTIONf_angle_d1.209870
X-RAY DIFFRACTIONf_dihedral_angle_d10.42189
X-RAY DIFFRACTIONf_chiral_restr0.08787
X-RAY DIFFRACTIONf_plane_restr0.007115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.550.3816880.32641695X-RAY DIFFRACTION52
1.55-1.770.31671570.25053110X-RAY DIFFRACTION95
1.77-2.230.29811470.26233271X-RAY DIFFRACTION100
2.23-44.190.21931790.14743322X-RAY DIFFRACTION100

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