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- PDB-6nyi: Crystal structure of computationally designed protein XXA -

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Basic information

Entry
Database: PDB / ID: 6nyi
TitleCrystal structure of computationally designed protein XXA
ComponentsDesign construct XXA
KeywordsDE NOVO PROTEIN / homotrimer / helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWei, K.Y. / Bick, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124169 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM124149 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Computational design of closely related proteins that adopt two well-defined but structurally divergent folds.
Authors: Wei, K.Y. / Moschidi, D. / Bick, M.J. / Nerli, S. / McShan, A.C. / Carter, L.P. / Huang, P.S. / Fletcher, D.A. / Sgourakis, N.G. / Boyken, S.E. / Baker, D.
History
DepositionFeb 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Design construct XXA
B: Design construct XXA
C: Design construct XXA


Theoretical massNumber of molelcules
Total (without water)33,2333
Polymers33,2333
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-94 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.403, 51.213, 48.838
Angle α, β, γ (deg.)90.000, 102.450, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Design construct XXA


Mass: 11077.787 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16 M magnesium acetate, 0.08 M sodium cacodylate pH 6.5, 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1111 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1111 Å / Relative weight: 1
ReflectionResolution: 2.17→63.181 Å / Num. obs: 16412 / % possible obs: 98.68 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.065 / Rrim(I) all: 0.169 / Net I/σ(I): 7.8
Reflection shellResolution: 2.17→2.25 Å / Rmerge(I) obs: 2.228 / Num. unique obs: 1457 / CC1/2: 0.526 / Rpim(I) all: 0.973 / Rrim(I) all: 2.439 / % possible all: 88.52

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Processing

Software
NameVersionClassification
PHENIXdev_3026refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→63.181 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 35.41
RfactorNum. reflection% reflection
Rfree0.281 1312 10.13 %
Rwork0.2588 --
obs0.2611 12952 92.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.53 Å2 / Biso mean: 56.5233 Å2 / Biso min: 31.57 Å2
Refinement stepCycle: final / Resolution: 2.3→63.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 0 30 2107
Biso mean---49.08 -
Num. residues----286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.39210.4411250.4291139126482
2.3921-2.5010.44781370.3521211134887
2.501-2.63290.33151380.32511239137788
2.6329-2.79780.33971480.30691238138690
2.7978-3.01390.28811440.2731303144792
3.0139-3.31710.29471510.26981335148696
3.3171-3.79710.25681510.23671358150997
3.7971-4.78370.22041570.19531398155598
4.7837-63.20460.26111610.24121419158098

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