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- PDB-8pri: The structure of nvBagel9 -

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Basic information

Entry
Database: PDB / ID: 8pri
TitleThe structure of nvBagel9
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: 2.1 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


Theoretical massNumber of molelcules
Total (without water)9,0511
Polymers9,0511
Non-polymers00
Water43224
1
A: Cell surface protein

A: Cell surface protein

A: Cell surface protein

A: Cell surface protein


Theoretical massNumber of molelcules
Total (without water)36,2044
Polymers36,2044
Non-polymers00
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 area5660 Å2
ΔGint-39 kcal/mol
Surface area12220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.713, 63.713, 37.838
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 (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M Sodium HEPES pH 7.5, 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: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Feb 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.1→32.53 Å / Num. obs: 4516 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.986 / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.101 / Rrim(I) all: 0.253 / Χ2: 1.02 / Net I/σ(I): 8.4 / Num. measured all: 28586
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.799 / Num. measured all: 2317 / Num. unique obs: 354 / CC1/2: 0.897 / Rpim(I) all: 0.339 / Rrim(I) all: 0.869 / Χ2: 1.13 / Net I/σ(I) obs: 3.7

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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: 2.1→32.53 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2657 253 5.6 %
Rwork0.1958 --
obs0.1994 4515 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→32.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms612 0 0 24 636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.056
X-RAY DIFFRACTIONf_dihedral_angle_d7.77185
X-RAY DIFFRACTIONf_chiral_restr0.06286
X-RAY DIFFRACTIONf_plane_restr0.007111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.650.2951240.2092103X-RAY DIFFRACTION100
2.65-32.530.25371290.1912159X-RAY DIFFRACTION100

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