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- PDB-6yqy: Crystal structure of sTIM11noCys, a de novo designed TIM barrel -

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Entry
Database: PDB / ID: 6yqy
TitleCrystal structure of sTIM11noCys, a de novo designed TIM barrel
Componentsde novo designed TIM barrel sTIM11noCys
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: 1.876 Å
AuthorsRomero-Romero, S. / Wiese, G.J. / 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 1.3Jan 24, 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

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Assembly

Deposited unit
A: de novo designed TIM barrel sTIM11noCys


Theoretical massNumber of molelcules
Total (without water)22,9171
Polymers22,9171
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.452, 50.452, 132.412
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-230-

HOH

21A-236-

HOH

31A-246-

HOH

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Components

#1: Protein de novo designed TIM barrel sTIM11noCys


Mass: 22917.422 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: pET21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.85 Å3/Da / Density % sol: 33.39 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium sulfate, 0.1 M Trisodium citrate pH: 5.6, 25% w/v PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.876→47.15 Å / Num. obs: 14703 / % possible obs: 99.9 % / Redundancy: 23.3 % / Biso Wilson estimate: 41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Net I/σ(I): 27
Reflection shellResolution: 1.876→1.94 Å / Redundancy: 23.2 % / Rmerge(I) obs: 1.281 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1410 / CC1/2: 0.81 / % possible all: 99

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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: 5BVL

5bvl


Resolution: 1.876→47.146 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.28
RfactorNum. reflection% reflection
Rfree0.2701 708 4.82 %
Rwork0.2202 --
obs0.2226 14703 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.3 Å2 / Biso mean: 54.2617 Å2 / Biso min: 21.9 Å2
Refinement stepCycle: final / Resolution: 1.876→47.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 0 49 1478
Biso mean---62.75 -
Num. residues----178
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.876-2.02070.34281460.2571268599
2.0207-2.2240.3161290.22092738100
2.224-2.54580.31451390.22692778100
2.5458-3.20740.28831440.25432801100
3.2074-100.24521500.20472993100
Refinement TLS params.Method: refined / Origin x: -15.6478 Å / Origin y: 7.9733 Å / Origin z: 4.985 Å
111213212223313233
T0.2405 Å2-0.0126 Å20.0351 Å2-0.2322 Å2-0.0707 Å2--0.2302 Å2
L4.435 °20.3082 °2-1.3105 °2-2.0029 °2-0.5135 °2--2.7595 °2
S-0.0221 Å °-0.2764 Å °0.1445 Å °0.0746 Å °0.0222 Å °-0.0075 Å °-0.1235 Å °-0.0019 Å °0.0033 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 183
2X-RAY DIFFRACTION1allB1 - 88

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