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- PDB-6nx2: Crystal structure of computationally designed protein AAA -

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Basic information

Entry
Database: PDB / ID: 6nx2
TitleCrystal structure of computationally designed protein AAA
ComponentsDesign construct AAA
KeywordsDE NOVO PROTEIN / homotrimer / helix
Function / homologyBROMIDE ION
Function and homology information
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 7, 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Design construct AAA
B: Design construct AAA
C: Design construct AAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6215
Polymers33,4613
Non-polymers1602
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-63 kcal/mol
Surface area14600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.592, 51.650, 85.527
Angle α, β, γ (deg.)90.00, 110.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Design construct AAA


Mass: 11153.590 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.03 M of each halide (sodium fluoride, sodium bromide, sodium iodide), 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999933 Å / Relative weight: 1
ReflectionResolution: 2.23→70 Å / Num. obs: 16424 / % possible obs: 98.4 % / Redundancy: 3.6 % / Net I/σ(I): 16.1
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 0.8 / % possible all: 86.9

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Processing

Software
NameVersionClassification
PHENIXDEV_2611refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ROSETTA MODEL

Resolution: 2.3→44.04 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 36.99
RfactorNum. reflection% reflection
Rfree0.279 1486 10.04 %
Rwork0.259 --
obs0.261 14808 90.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 93.19 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 2 11 1957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051947
X-RAY DIFFRACTIONf_angle_d0.5082643
X-RAY DIFFRACTIONf_dihedral_angle_d18.6171227
X-RAY DIFFRACTIONf_chiral_restr0.033327
X-RAY DIFFRACTIONf_plane_restr0.003363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3031-2.37750.4392980.3997916X-RAY DIFFRACTION69
2.3775-2.46240.43941080.35151027X-RAY DIFFRACTION76
2.4624-2.5610.33331260.30551112X-RAY DIFFRACTION83
2.561-2.67760.28871280.30491181X-RAY DIFFRACTION88
2.6776-2.81870.36811390.28161209X-RAY DIFFRACTION92
2.8187-2.99530.30251430.29061250X-RAY DIFFRACTION94
2.9953-3.22650.3421470.3111294X-RAY DIFFRACTION97
3.2265-3.5510.2661450.24351311X-RAY DIFFRACTION99
3.551-4.06460.24041500.21891360X-RAY DIFFRACTION99
4.0646-5.11970.19791500.20181340X-RAY DIFFRACTION99
5.1197-44.05240.32841520.2991322X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2848-0.201-0.45290.1603-1.35872.4107-0.2259-0.12970.10470.0604-0.21120.0806-0.5821-0.5723-0.00240.5671-0.0143-0.00060.5989-0.04120.5435-3.32780.970438.703
20.99120.2544-0.768-0.14220.78031.8419-0.0318-0.20110.02790.1996-0.2962-0.0592-0.52040.9098-0.00130.7209-0.0551-0.02830.5074-0.01910.61382.21622.779539.1928
30.00380.40551.26280.6846-0.47122.2257-0.305-0.0049-0.06030.1603-0.15550.00081.25730.0931-0.00130.55760.077-0.00630.5917-0.01020.54821.1649-2.669938.7593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 4 THROUGH 92)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 4 THROUGH 92)
3X-RAY DIFFRACTION3(CHAIN 'C' AND RESID 4 THROUGH 92)

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