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- PDB-8prt: The structure of nvBagel8 in the presence of Co(II) -

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Basic information

Entry
Database: PDB / ID: 8prt
TitleThe structure of nvBagel8 in the presence of Co(II)
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 / 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: 1.65 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 nvBagel8 in the presence of Co(II)
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
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1693
Polymers9,0511
Non-polymers1182
Water1,910106
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)36,67512
Polymers36,2044
Non-polymers4718
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 area5960 Å2
ΔGint-38 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.993, 55.993, 108.192
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-101-

CO

21A-102-

CO

31A-220-

HOH

41A-299-

HOH

51A-306-

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
Details: nvBagel8 / 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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.5
Details: 0.0085 M Cobalt chloride, 0.085 M MES pH 6.5, 1.53 M Ammonium sulfate, 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: 0.97629 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: 0.97629 Å / Relative weight: 1
ReflectionResolution: 1.65→39.59 Å / Num. obs: 19762 / % possible obs: 100 % / Redundancy: 23 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.02 / Rrim(I) all: 0.094 / Χ2: 0.89 / Net I/σ(I): 22.4
Reflection shellResolution: 1.65→1.68 Å / % possible obs: 100 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.723 / Num. measured all: 10921 / Num. unique obs: 510 / CC1/2: 0.978 / Rpim(I) all: 0.157 / Rrim(I) all: 0.74 / Χ2: 0.68 / Net I/σ(I) obs: 4.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→39.59 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1885 930 4.71 %
Rwork0.1371 --
obs0.1397 19762 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms612 0 2 106 720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009665
X-RAY DIFFRACTIONf_angle_d1.093908
X-RAY DIFFRACTIONf_dihedral_angle_d6.23391
X-RAY DIFFRACTIONf_chiral_restr0.06589
X-RAY DIFFRACTIONf_plane_restr0.008120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.740.23381300.15872687X-RAY DIFFRACTION100
1.74-1.850.20111370.13492683X-RAY DIFFRACTION100
1.85-1.990.17491370.11722672X-RAY DIFFRACTION100
1.99-2.190.18721260.13142684X-RAY DIFFRACTION100
2.19-2.50.16911130.1442735X-RAY DIFFRACTION100
2.51-3.160.17811360.15192682X-RAY DIFFRACTION100
3.16-39.590.19541510.132689X-RAY DIFFRACTION100

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