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- PDB-6yqx: Crystal structure of DeNovoTIM13, a de novo designed TIM barrel -

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Entry
Database: PDB / ID: 6yqx
TitleCrystal structure of DeNovoTIM13, a de novo designed TIM barrel
Componentsde novo designed TIM barrel DeNovoTIM13
KeywordsDE NOVO PROTEIN / de novo protein design / epistasis / stability landscape / TIM barrel / (beta/alfa)8 barrel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.638 Å
AuthorsRomero-Romero, S. / Kordes, S. / Shanmugaratnam, S. / Fernandez-Velasco, D.A. / Hocker, B.
Funding support Mexico, 2items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)254514 Mexico
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN220516 Mexico
CitationJournal: J.Mol.Biol. / Year: 2021
Title: The Stability Landscape of de novo TIM Barrels Explored by a Modular Design Approach.
Authors: Romero-Romero, S. / Costas, M. / Silva Manzano, D.A. / Kordes, S. / Rojas-Ortega, E. / Tapia, C. / Guerra, Y. / Shanmugaratnam, S. / Rodriguez-Romero, A. / Baker, D. / Hocker, B. / Fernandez-Velasco, D.A.
History
DepositionApr 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: de novo designed TIM barrel DeNovoTIM13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2453
Polymers22,1181
Non-polymers1282
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-12 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.722, 51.722, 63.968
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein de novo designed TIM barrel DeNovoTIM13


Mass: 22117.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: M (N-terminal) and GLEHHHHHH (C-terminal) come from the expresion vector.
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.17 M sodium acetate, 0.085 M TRIS pH: 8.5, 25% 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: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 11, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.638→44.793 Å / Num. obs: 23407 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Net I/σ(I): 14.3
Reflection shellResolution: 1.638→1.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2280 / CC1/2: 0.659 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIX1.15_3459phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rosetta backbone model

Resolution: 1.638→44.793 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 20.68
RfactorNum. reflection% reflection
Rfree0.2014 1983 8.47 %
Rwork0.1714 --
obs0.1738 23405 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.67 Å2 / Biso mean: 39.2143 Å2 / Biso min: 16.68 Å2
Refinement stepCycle: final / Resolution: 1.638→44.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 7 131 1579
Biso mean--61.34 53.69 -
Num. residues----181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6384-1.67940.32691460.2739148897
1.6794-1.72480.27171450.26481539100
1.7248-1.77560.27451400.23471553100
1.7756-1.83290.25681390.21971521100
1.8329-1.89840.25841460.2081525100
1.8984-1.97440.23861400.19771527100
1.9744-2.06420.22591460.1921554100
2.0642-2.17310.20511420.17451528100
2.1731-2.30920.18591440.1688151299
2.3092-2.48750.20451480.1768154499
2.4875-2.73780.21961430.17221540100
2.7378-3.13390.20511350.18191520100
3.1339-3.9480.21221360.1473154699
3.948-100.15411330.1528152599
Refinement TLS params.Method: refined / Origin x: 4.2974 Å / Origin y: 16.4939 Å / Origin z: -2.6164 Å
111213212223313233
T0.1724 Å2-0.037 Å20.0167 Å2-0.1631 Å20.0297 Å2--0.1804 Å2
L2.1456 °2-0.8906 °2-0.1374 °2-2.9797 °21.0604 °2--2.5679 °2
S0.0262 Å °-0.0605 Å °-0.2594 Å °0.1231 Å °-0.1149 Å °0.1501 Å °0.1907 Å °-0.1388 Å °0.0595 Å °
Refinement TLS groupSelection details: (chain A and resseq 2:184)

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