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- PDB-6v50: Coiled-coil Trimer with Glu:Ser:Lys Triad with K7A mutation -

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Basic information

Entry
Database: PDB / ID: 6v50
TitleCoiled-coil Trimer with Glu:Ser:Lys Triad with K7A mutation
ComponentsCoiled-coil Trimer with Glu:Ser:Lys Triad with K7A mutation
KeywordsDE NOVO PROTEIN / Trimer / Helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.285 Å
AuthorsSmith, M.S. / Stern, K.L. / Billings, W.M. / Price, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR15 GM116055-01 United States
CitationJournal: Biochemistry / Year: 2020
Title: Context-Dependent Stabilizing Interactions among Solvent-Exposed Residues along the Surface of a Trimeric Helix Bundle.
Authors: Stern, K.L. / Smith, M.S. / Billings, W.M. / Loftus, T.J. / Conover, B.M. / Della Corte, D. / Price, J.L.
History
DepositionDec 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coiled-coil Trimer with Glu:Ser:Lys Triad with K7A mutation
B: Coiled-coil Trimer with Glu:Ser:Lys Triad with K7A mutation


Theoretical massNumber of molelcules
Total (without water)7,1362
Polymers7,1362
Non-polymers00
Water28816
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A: Coiled-coil Trimer with Glu:Ser:Lys Triad with K7A mutation

A: Coiled-coil Trimer with Glu:Ser:Lys Triad with K7A mutation

A: Coiled-coil Trimer with Glu:Ser:Lys Triad with K7A mutation


Theoretical massNumber of molelcules
Total (without water)10,7043
Polymers10,7043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area3710 Å2
ΔGint-31 kcal/mol
Surface area6400 Å2
MethodPISA
2
B: Coiled-coil Trimer with Glu:Ser:Lys Triad with K7A mutation

B: Coiled-coil Trimer with Glu:Ser:Lys Triad with K7A mutation

B: Coiled-coil Trimer with Glu:Ser:Lys Triad with K7A mutation


Theoretical massNumber of molelcules
Total (without water)10,7043
Polymers10,7043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3690 Å2
ΔGint-31 kcal/mol
Surface area6290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.190, 39.190, 98.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein/peptide Coiled-coil Trimer with Glu:Ser:Lys Triad with K7A mutation


Mass: 3568.031 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 40% PEG300, 100 mM HEPES/NaOH, pH 7.5, 200 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5406 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Apr 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.285→19.946 Å / Num. obs: 5113 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.029 / Rrim(I) all: 0.104 / Net I/σ(I): 12
Reflection shellResolution: 2.285→2.615 Å / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 258 / CC1/2: 0.946 / Rpim(I) all: 0.135 / Rrim(I) all: 0.104

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6OVS

6ovs


Resolution: 2.285→19.946 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.79
RfactorNum. reflection% reflection
Rfree0.2657 486 9.51 %
Rwork0.1965 --
obs0.2028 5113 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.48 Å2 / Biso mean: 27.252 Å2 / Biso min: 11.71 Å2
Refinement stepCycle: final / Resolution: 2.285→19.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms502 0 0 16 518
Biso mean---27.86 -
Num. residues----64
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006506
X-RAY DIFFRACTIONf_angle_d0.677676
X-RAY DIFFRACTIONf_chiral_restr0.02976
X-RAY DIFFRACTIONf_plane_restr0.00386
X-RAY DIFFRACTIONf_dihedral_angle_d2.111316
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.285-2.6150.3081680.2141154699
2.615-3.29220.30261680.2271538100
3.2922-19.9460.22581500.17271543100

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