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- PDB-6nz3: Crystal structure of computationally designed protein XAA_GGHN -

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Basic information

Entry
Database: PDB / ID: 6nz3
TitleCrystal structure of computationally designed protein XAA_GGHN
ComponentsDesign construct XAA_GGHN
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 12, 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 XAA_GGHN
B: Design construct XAA_GGHN
C: Design construct XAA_GGHN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9114
Polymers32,8763
Non-polymers351
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9000 Å2
ΔGint-110 kcal/mol
Surface area13730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.741, 51.271, 85.873
Angle α, β, γ (deg.)90.000, 110.080, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Design construct XAA_GGHN


Mass: 10958.525 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#3: 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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 10.5 / Details: 0.1 M CAPS pH 10.5, 40% (v/v) MPD

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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: Sep 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1111 Å / Relative weight: 1
ReflectionResolution: 1.66→80.66 Å / Num. obs: 34486 / % possible obs: 80.71 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.015 / Rrim(I) all: 0.039 / Net I/σ(I): 14.4
Reflection shellResolution: 1.66→1.72 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1008 / % possible all: 23.64

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→80.655 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 33.89
RfactorNum. reflection% reflection
Rfree0.3017 922 5.76 %
Rwork0.262 --
obs0.2641 16014 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.43 Å2 / Biso mean: 69.3967 Å2 / Biso min: 40.69 Å2
Refinement stepCycle: final / Resolution: 2.3→80.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 1 10 2041
Biso mean--56.69 60.62 -
Num. residues----275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.42130.29131350.25862088222396
2.4213-2.5730.35481270.27642138226597
2.573-2.77160.39531300.29952122225298
2.7716-3.05060.34781260.29262181230799
3.0506-3.4920.30131300.28472156228699
3.492-4.39950.2531420.233921922334100
4.3995-80.70480.31021320.25642215234797

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