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- PDB-6v5g: Coiled-coil Trimer with Ala:Leu:Lys Triad -

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Basic information

Entry
Database: PDB / ID: 6v5g
TitleCoiled-coil Trimer with Ala:Leu:Lys Triad
ComponentsCoiled-coil Trimer with Ala:Leu:Lys Triad
KeywordsDE NOVO PROTEIN / Trimer / Helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 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 4, 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 1.3Nov 6, 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 Ala:Leu:Lys Triad
B: Coiled-coil Trimer with Ala:Leu:Lys Triad
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8553
Polymers7,6172
Non-polymers2381
Water1,65792
1
A: Coiled-coil Trimer with Ala:Leu:Lys Triad
hetero molecules

A: Coiled-coil Trimer with Ala:Leu:Lys Triad
hetero molecules

A: Coiled-coil Trimer with Ala:Leu:Lys Triad
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1406
Polymers11,4253
Non-polymers7153
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 area4620 Å2
ΔGint-33 kcal/mol
Surface area7230 Å2
MethodPISA
2
B: Coiled-coil Trimer with Ala:Leu:Lys Triad

B: Coiled-coil Trimer with Ala:Leu:Lys Triad

B: Coiled-coil Trimer with Ala:Leu:Lys Triad


Theoretical massNumber of molelcules
Total (without water)11,4253
Polymers11,4253
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 area3700 Å2
ΔGint-29 kcal/mol
Surface area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.178, 38.178, 102.772
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 Ala:Leu:Lys Triad


Mass: 3808.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.89 Å3/Da / Density % sol: 35 %
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: Aug 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.68→31.48 Å / Num. obs: 6377 / % possible obs: 99.8 % / Redundancy: 3.9 % / CC1/2: 0.813 / Rmerge(I) obs: 0.373 / Rpim(I) all: 0.157 / Rrim(I) all: 0.407 / Net I/σ(I): 10.2
Reflection shellResolution: 1.68→1.7686 Å / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1035 / CC1/2: 0.606 / Rpim(I) all: 0.384 / Rrim(I) all: 0.622

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Processing

Software
NameVersionClassification
PHENIXdev_2906refinement
PDB_EXTRACT3.25data extraction
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UXT

5uxt


Resolution: 1.68→31.48 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 24.29
RfactorNum. reflection% reflection
Rfree0.2294 983 10.09 %
Rwork0.1731 --
obs0.1785 6377 76.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 44.87 Å2 / Biso mean: 15.5606 Å2 / Biso min: 4.86 Å2
Refinement stepCycle: final / Resolution: 1.68→31.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms536 0 38 92 666
Biso mean--24.68 23.49 -
Num. residues----68
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6801-1.76860.30741150.2811103562
1.7686-1.87920.28721290.2105108767
1.8792-2.02410.24451290.1902118472
2.0241-2.22740.21081420.1526121975
2.2274-2.54880.22171470.1507134080
2.5488-3.20780.2321370.1688140486
3.2078-17.1290.21481840.1678149492

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