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- PDB-6nye: Crystal structure of computationally designed protein XAX -

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Basic information

Entry
Database: PDB / ID: 6nye
TitleCrystal structure of computationally designed protein XAX
ComponentsDesign construct XAX
KeywordsDE NOVO PROTEIN / homotrimer / helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
B: Design construct XAX
C: Design construct XAX


Theoretical massNumber of molelcules
Total (without water)33,1853
Polymers33,1853
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-94 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.179, 75.322, 96.944
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Design construct XAX


Mass: 11061.786 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


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.99 Å3/Da / Density % sol: 38.14 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium acetate, 20% (w/v) PEG 3350

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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: Oct 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1111 Å / Relative weight: 1
ReflectionResolution: 1.8→96.94 Å / Num. obs: 23968 / % possible obs: 97.28 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.038 / Rrim(I) all: 0.131 / Net I/σ(I): 11.4
Reflection shellResolution: 1.8→1.87 Å / Rmerge(I) obs: 3.464 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1839 / CC1/2: 0.107 / Rpim(I) all: 1.69 / Rrim(I) all: 3.879 / % possible all: 75.99

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Processing

Software
NameVersionClassification
PHENIXdev_2849refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→59.479 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.82
RfactorNum. reflection% reflection
Rfree0.2335 1703 8.36 %
Rwork0.2019 --
obs0.2046 20362 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.8 Å2 / Biso mean: 34.4008 Å2 / Biso min: 18.19 Å2
Refinement stepCycle: final / Resolution: 1.9→59.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 0 176 2295
Biso mean---36.26 -
Num. residues----283
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.95590.36351260.36621370149687
1.9559-2.01910.31911280.27671460158893
2.0191-2.09120.26221350.24441504163995
2.0912-2.1750.27671410.22191520166197
2.175-2.2740.25361430.19891532167597
2.274-2.39380.21351420.18611545168797
2.3938-2.54380.23781460.19031567171398
2.5438-2.74020.22051420.19621576171899
2.7402-3.0160.26021470.20431599174699
3.016-3.45240.22311460.19651618176499
3.4524-4.34940.17131500.164216321782100
4.3494-59.50820.24581570.204917361893100

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