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- PDB-6v58: Coiled-coil Trimer with Glu:Norleucine:Lys Triad -

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Basic information

Entry
Database: PDB / ID: 6v58
TitleCoiled-coil Trimer with Glu:Norleucine:Lys Triad
ComponentsCoiled-coil Trimer with Glu:Norleucine:Lys Triad
KeywordsDE NOVO PROTEIN / Trimer / Helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.201 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 3, 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 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 23, 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:
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Assembly

Deposited unit
A: Coiled-coil Trimer with Glu:Norleucine:Lys Triad
B: Coiled-coil Trimer with Glu:Norleucine:Lys Triad


Theoretical massNumber of molelcules
Total (without water)7,7332
Polymers7,7332
Non-polymers00
Water41423
1
A: Coiled-coil Trimer with Glu:Norleucine:Lys Triad

A: Coiled-coil Trimer with Glu:Norleucine:Lys Triad

A: Coiled-coil Trimer with Glu:Norleucine:Lys Triad


Theoretical massNumber of molelcules
Total (without water)11,5993
Polymers11,5993
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 area4000 Å2
ΔGint-29 kcal/mol
Surface area6340 Å2
MethodPISA
2
B: Coiled-coil Trimer with Glu:Norleucine:Lys Triad

B: Coiled-coil Trimer with Glu:Norleucine:Lys Triad

B: Coiled-coil Trimer with Glu:Norleucine:Lys Triad


Theoretical massNumber of molelcules
Total (without water)11,5993
Polymers11,5993
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 area3890 Å2
ΔGint-33 kcal/mol
Surface area6710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.068, 39.068, 113.331
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-111-

HOH

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Components

#1: Protein/peptide Coiled-coil Trimer with Glu:Norleucine:Lys Triad


Mass: 3866.458 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.: 23 / 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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 40% v/v PEG600, 100 mM sodium citrate tribasic/citric acid, pH 5.5

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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: Dec 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.2→37.78 Å / Num. obs: 3261 / % possible obs: 99.5 % / Redundancy: 4.6 % / CC1/2: 0.977 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.051 / Rrim(I) all: 0.128 / Net I/σ(I): 16.2
Reflection shellResolution: 2.2→2.42 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1210 / CC1/2: 0.796 / Rpim(I) all: 0.248 / Rrim(I) all: 0.408

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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: 2.201→37.78 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 32
RfactorNum. reflection% reflection
Rfree0.2791 580 9.54 %
Rwork0.2036 --
obs0.2111 3261 92.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.57 Å2 / Biso mean: 38.0147 Å2 / Biso min: 21.12 Å2
Refinement stepCycle: final / Resolution: 2.201→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms533 0 0 23 556
Biso mean---41.78 -
Num. residues----67
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2014-2.42240.30821210.2049121081
2.4224-2.77170.30771350.2352137893
2.7717-3.48740.32451580.2167143198
3.4874-37.780.24221660.1871147899

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