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- PDB-6ny8: Crystal structure of computationally designed protein XAA_GVDQ wi... -

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Basic information

Entry
Database: PDB / ID: 6ny8
TitleCrystal structure of computationally designed protein XAA_GVDQ with calcium
ComponentsDesign construct XAA_GVDQ
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 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,0505
Polymers32,9753
Non-polymers762
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-114 kcal/mol
Surface area14110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.158, 49.602, 85.032
Angle α, β, γ (deg.)90.00, 109.71, 90.00
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) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.05 M calcium acetate, 0.1 M sodium acetate pH 4.5, 40% (w/v) 1,2-propanediol

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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 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: 1.97→80.05 Å / Num. obs: 23465 / % possible obs: 97.91 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Net I/σ(I): 12.8
Reflection shellResolution: 1.97→2.04 Å / Rmerge(I) obs: 6.11 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 2125 / CC1/2: 0.255 / Rpim(I) all: 2.751 / Rrim(I) all: 6.727 / % possible all: 89.55

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Processing

Software
NameVersionClassification
PHENIX(dev_2849: ???)refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→80.049 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 39.86
RfactorNum. reflection% reflection
Rfree0.3041 1234 8.58 %
Rwork0.2875 --
obs0.289 14387 94.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→80.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 2 0 1917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.39230.44621230.41991310X-RAY DIFFRACTION85
2.3923-2.50120.4091210.36341371X-RAY DIFFRACTION89
2.5012-2.6330.35431330.32341403X-RAY DIFFRACTION92
2.633-2.7980.33341360.29481446X-RAY DIFFRACTION94
2.798-3.01410.26821350.28911441X-RAY DIFFRACTION95
3.0141-3.31740.30741460.30751539X-RAY DIFFRACTION98
3.3174-3.79740.29231440.26831533X-RAY DIFFRACTION99
3.7974-4.78430.25061470.24211555X-RAY DIFFRACTION100
4.7843-80.09710.33461490.31011555X-RAY DIFFRACTION97

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