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- PDB-8prc: The structure of v13Bagel8 -

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Basic information

Entry
Database: PDB / ID: 8prc
TitleThe structure of v13Bagel8
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: 2.35 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 v13Bagel8
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)9,3044
Polymers9,1081
Non-polymers1963
Water23413
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)37,21716
Polymers36,4324
Non-polymers78512
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 area7890 Å2
ΔGint-57 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.159, 54.159, 109.537
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-103-

ZN

21A-211-

HOH

31A-213-

HOH

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Components

#1: Protein Cell surface protein


Mass: 9107.999 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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.5
Details: 0.16 M Zinc acetate, 0.08 M Sodium cacodylate pH 6.5, 14.4 %(w/v) PEG 8000, 20 %(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: 0.976292 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: 0.976292 Å / Relative weight: 1
ReflectionResolution: 2.35→48.55 Å / Num. obs: 6417 / % possible obs: 100 % / Redundancy: 25.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.028 / Rrim(I) all: 0.138 / Χ2: 1.02 / Net I/σ(I): 19.6
Reflection shellResolution: 2.35→2.43 Å / % possible obs: 100 % / Redundancy: 26.8 % / Rmerge(I) obs: 0.634 / Num. measured all: 9240 / Num. unique obs: 345 / CC1/2: 0.994 / Rpim(I) all: 0.124 / Rrim(I) all: 0.646 / Χ2: 0.99 / Net I/σ(I) obs: 4.6

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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: 2.35→38.3 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3118 333 5.19 %
Rwork0.2384 --
obs0.242 6417 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→38.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms612 0 3 13 628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008631
X-RAY DIFFRACTIONf_angle_d0.9857
X-RAY DIFFRACTIONf_dihedral_angle_d7.37385
X-RAY DIFFRACTIONf_chiral_restr0.05786
X-RAY DIFFRACTIONf_plane_restr0.006111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.960.34041630.30643007X-RAY DIFFRACTION98
2.96-38.30.30341700.2163077X-RAY DIFFRACTION100

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