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- PDB-6wvs: Hyperstable de novo TIM barrel variant DeNovoTIM15 -

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Entry
Database: PDB / ID: 6wvs
TitleHyperstable de novo TIM barrel variant DeNovoTIM15
ComponentsDeNovoTIM15 hyperstable de novo TIM barrel
KeywordsDE NOVO PROTEIN / TIM barrel / hyperstable / symmetric / de novo / repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsBick, M.J. / Haydon, I.C. / Caldwell, S.J. / Zeymer, C. / Huang, P. / Fernandez-Velasco, D.A. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)HDTRA1-19-1-0003 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion.
Authors: Caldwell, S.J. / Haydon, I.C. / Piperidou, N. / Huang, P.S. / Bick, M.J. / Sjostrom, H.S. / Hilvert, D. / Baker, D. / Zeymer, C.
History
DepositionMay 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity / struct
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _struct.title
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: DeNovoTIM15 hyperstable de novo TIM barrel


Theoretical massNumber of molelcules
Total (without water)21,8241
Polymers21,8241
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.199, 53.199, 64.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein DeNovoTIM15 hyperstable de novo TIM barrel


Mass: 21824.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.02 M each of each 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol, 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.202→37.44 Å / Num. obs: 10232 / % possible obs: 99.54 % / Redundancy: 9.1 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.2038 / Rpim(I) all: 0.07193 / Rrim(I) all: 0.2163 / Net I/σ(I): 8.32
Reflection shellResolution: 2.202→2.281 Å / Redundancy: 8.2 % / Rmerge(I) obs: 2.759 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 7829 / CC1/2: 0.558 / CC star: 0.846 / Rpim(I) all: 1.015 / Rrim(I) all: 2.943 / % possible all: 97.44

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Processing

Software
NameVersionClassification
PHENIX1.18rc2_3793refinement
DENZOdata reduction
PHASERphasing
Cootmodel building
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rosetta design model of protein

Resolution: 2.202→37.44 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2046 982 9.61 %
Rwork0.192 9238 -
obs0.2025 10220 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.91 Å2
Refinement stepCycle: LAST / Resolution: 2.202→37.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 0 19 1310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271296
X-RAY DIFFRACTIONf_angle_d0.50941764
X-RAY DIFFRACTIONf_chiral_restr0.0475235
X-RAY DIFFRACTIONf_plane_restr0.0029222
X-RAY DIFFRACTIONf_dihedral_angle_d13.7919189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.320.57341460.51561286X-RAY DIFFRACTION88.08
2.32-2.460.26451330.3011307X-RAY DIFFRACTION90.58
2.46-2.650.28151410.28281346X-RAY DIFFRACTION90.4
2.66-2.920.26811460.26591303X-RAY DIFFRACTION89.86
2.92-3.340.20351490.21931329X-RAY DIFFRACTION89.86
3.34-4.210.19351410.16441328X-RAY DIFFRACTION90.4
4.21-37.440.17371260.15111339X-RAY DIFFRACTION90.72

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