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- PDB-6nxm: Crystal structure of computationally designed protein XAA_GVDQ -

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Basic information

Entry
Database: PDB / ID: 6nxm
TitleCrystal structure of computationally designed protein XAA_GVDQ
ComponentsDesign construct XAA_GVDQ
KeywordsDE NOVO PROTEIN / homotrimer / helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 8, 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_GVDQ
B: Design construct XAA_GVDQ
C: Design construct XAA_GVDQ


Theoretical massNumber of molelcules
Total (without water)32,9753
Polymers32,9753
Non-polymers00
Water1086
1
A: Design construct XAA_GVDQ
B: Design construct XAA_GVDQ
C: Design construct XAA_GVDQ

A: Design construct XAA_GVDQ
B: Design construct XAA_GVDQ
C: Design construct XAA_GVDQ


Theoretical massNumber of molelcules
Total (without water)65,9496
Polymers65,9496
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area19800 Å2
ΔGint-220 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.045, 58.282, 58.793
Angle α, β, γ (deg.)90.000, 125.050, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Design construct XAA_GVDQ


Mass: 10991.570 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2.0 M sodium formate, 0.1 M sodium acetate pH 4.6

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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: 1.82→48.133 Å / Num. obs: 23257 / % possible obs: 92.44 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.018 / Rrim(I) all: 0.045 / Net I/σ(I): 14.1
Reflection shellResolution: 1.82→1.89 Å / Num. unique obs: 1365 / CC1/2: 0.011 / % possible all: 54.62

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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: 2.2→48.133 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 36.84
RfactorNum. reflection% reflection
Rfree0.277 1200 8.68 %
Rwork0.2457 --
obs0.2483 13830 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.42 Å2 / Biso mean: 78.4719 Å2 / Biso min: 39.22 Å2
Refinement stepCycle: final / Resolution: 2.2→48.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 0 6 1874
Biso mean---68.55 -
Num. residues----274
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 (%)
2.2002-2.28830.46361160.39981301141790
2.2883-2.39240.4031240.35611327145193
2.3924-2.51860.37411440.3151404154895
2.5186-2.67630.36871340.28981404153897
2.6763-2.8830.37391310.27771390152197
2.883-3.1730.33751460.28031421156799
3.173-3.63210.32771350.26331462159799
3.6321-4.57540.18791370.189814531590100
4.5754-48.14480.23771330.22641468160197

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