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- PDB-6z2i: Crystal structure of DeNovoTIM6, a de novo designed TIM barrel -

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Basic information

Entry
Database: PDB / ID: 6z2i
TitleCrystal structure of DeNovoTIM6, a de novo designed TIM barrel
Componentsde novo designed TIM barrel DeNovoTIM6
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: 2.901 Å
AuthorsRomero-Romero, S. / Kordes, S. / Shanmugaratnam, S. / Rodriguez-Romero, A. / 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
DepositionMay 15, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: de novo designed TIM barrel DeNovoTIM6


Theoretical massNumber of molelcules
Total (without water)22,5541
Polymers22,5541
Non-polymers00
Water18010
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 area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.480, 87.480, 44.263
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4

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Components

#1: Protein de novo designed TIM barrel DeNovoTIM6


Mass: 22553.506 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.88 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.095 M Sodium citrate pH: 5.0, 19% v/v Isopropanol, 25% w/v PEG 4000, 5% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 31, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.901→30.93 Å / Num. obs: 7620 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 73.8 Å2 / CC1/2: 0.94 / Rmerge(I) obs: 0.18 / Net I/σ(I): 4.3
Reflection shellResolution: 2.901→3.01 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.195 / Mean I/σ(I) obs: 1 / Num. unique obs: 389 / CC1/2: 0.773 / % possible all: 100

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Processing

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

Resolution: 2.901→30.929 Å / SU ML: 0.62 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 41.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.372 760 10.03 %
Rwork0.3167 6821 -
obs0.3221 7581 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.43 Å2 / Biso mean: 89.2869 Å2 / Biso min: 24.55 Å2
Refinement stepCycle: final / Resolution: 2.901→30.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 0 10 1185
Biso mean---77.07 -
Num. residues----168
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.901-3.12430.40261500.35331356100
3.1243-3.43830.3871510.32561351100
3.4383-3.9350.3421540.2933135199
3.935-4.95440.38551500.30211377100
4.9544-100.36831550.3283138698
Refinement TLS params.Method: refined / Origin x: 22.2519 Å / Origin y: 5.1599 Å / Origin z: 5.3322 Å
111213212223313233
T0.1664 Å20.0801 Å20.0059 Å2-0.4111 Å20.0735 Å2--0.304 Å2
L2.2179 °20.0148 °20.003 °2-2.4936 °20.4914 °2--1.4105 °2
S0.2682 Å °0.2293 Å °-0.2582 Å °0.0725 Å °-0.0636 Å °-0.2862 Å °0.4435 Å °-0.0132 Å °0.0829 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 185
2X-RAY DIFFRACTION1allB1 - 10

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