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- PDB-8prh: The structure of nvBagel7 -

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Basic information

Entry
Database: PDB / ID: 8prh
TitleThe structure of nvBagel7
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: 1.6 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
Water1,13563
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_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area5500 Å2
ΔGint-40 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.131, 54.131, 49.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-122-

HOH

21A-159-

HOH

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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.: 63 / 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 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 5.6
Details: 0.17 M Ammonium acetate, 0.085 M tri-Sodium citrate pH 5.6, 25.5 %(w/v) PEG 4000, 15 %(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→54.13 Å / Num. obs: 10181 / % possible obs: 100 % / Redundancy: 24 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.011 / Rrim(I) all: 0.057 / Net I/σ(I): 38.3 / Num. measured all: 244109
Reflection shellResolution: 1.6→1.63 Å / % possible obs: 100 % / Redundancy: 18.6 % / Rmerge(I) obs: 0.243 / Num. measured all: 9268 / Num. unique obs: 499 / CC1/2: 0.988 / Rpim(I) all: 0.057 / Rrim(I) all: 0.25 / Net I/σ(I) obs: 6.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data scaling
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→38.28 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 18.87 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1956 516 5.08 %
Rwork0.1708 --
obs0.1721 10161 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→38.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms601 0 0 63 664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.114
X-RAY DIFFRACTIONf_dihedral_angle_d6.49191
X-RAY DIFFRACTIONf_chiral_restr0.07788
X-RAY DIFFRACTIONf_plane_restr0.008121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.760.17591210.14792346X-RAY DIFFRACTION100
1.76-2.020.20241260.16782374X-RAY DIFFRACTION100
2.02-2.540.19371300.16962384X-RAY DIFFRACTION100
2.54-38.280.19811390.17682541X-RAY DIFFRACTION100

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