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- PDB-6nyk: Crystal structure of computationally designed protein XAX_GGDQ -

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Basic information

Entry
Database: PDB / ID: 6nyk
TitleCrystal structure of computationally designed protein XAX_GGDQ
ComponentsDesign construct XAX_GGDQ
KeywordsDE NOVO PROTEIN / homotrimer / helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 XAX_GGDQ
B: Design construct XAX_GGDQ
C: Design construct XAX_GGDQ


Theoretical massNumber of molelcules
Total (without water)33,4853
Polymers33,4853
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-92 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.416, 55.002, 57.906
Angle α, β, γ (deg.)90.000, 123.380, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Design construct XAX_GGDQ


Mass: 11161.817 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)

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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: 1.89 Å3/Da / Density % sol: 35.08 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.0 M lithium chloride, 0.1 M MES pH 6.0, 20% (w/v) PEG 6000

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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: May 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1111 Å / Relative weight: 1
ReflectionResolution: 2.5→48.35 Å / Num. obs: 8627 / % possible obs: 98.18 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.103 / Rrim(I) all: 0.039 / Net I/σ(I): 6.7
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 4.228 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 821 / CC1/2: 0.187 / Rrim(I) all: 4.6 / Rsym value: 1.788 / % possible all: 97.16

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Processing

Software
NameVersionClassification
PHENIXdev_3112refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.35 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 41.12
RfactorNum. reflection% reflection
Rfree0.2971 604 10.11 %
Rwork0.2617 --
obs0.2656 5974 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 226.43 Å2 / Biso mean: 85.8214 Å2 / Biso min: 42.87 Å2
Refinement stepCycle: final / Resolution: 2.8→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1729 0 0 0 1729
Num. residues----271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-3.08180.36251290.28261302143191
3.0818-3.52760.29891470.24211312145995
3.5276-4.44390.22081650.22891397156298
4.4439-48.36050.33011630.28671359152295

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