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- PDB-6q25: Coiled-coil Trimer with Glu:Leu:Lys Triad -

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Basic information

Entry
Database: PDB / ID: 6q25
TitleCoiled-coil Trimer with Glu:Leu:Lys Triad
ComponentsCoiled-coil Trimer with Glu:Leu:Lys Triad
KeywordsDE NOVO PROTEIN / Trimer / Helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.893 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
DepositionAug 6, 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 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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:Leu:Lys Triad
B: Coiled-coil Trimer with Glu:Leu:Lys Triad


Theoretical massNumber of molelcules
Total (without water)7,7332
Polymers7,7332
Non-polymers00
Water1,36976
1
A: Coiled-coil Trimer with Glu:Leu:Lys Triad

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

A: Coiled-coil Trimer with Glu:Leu: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 area4130 Å2
ΔGint-37 kcal/mol
Surface area6360 Å2
MethodPISA
2
B: Coiled-coil Trimer with Glu:Leu:Lys Triad

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

B: Coiled-coil Trimer with Glu:Leu: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 area3900 Å2
ΔGint-33 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.063, 39.063, 101.522
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:Leu: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.: 76 / 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: 1.93 Å3/Da / Density % sol: 36.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50% PEG200, 100 mM HEPES free acid/NaOH, pH 7.5

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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: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.893→17.409 Å / Num. obs: 4584 / % possible obs: 98.94 % / Redundancy: 4.9 % / CC1/2: 0.948 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.087 / Rrim(I) all: 0.211 / Net I/σ(I): 9.9
Reflection shellResolution: 1.893→1.961 Å / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 469 / CC1/2: 0.668 / Rpim(I) all: 0.38 / Rrim(I) all: 0.658

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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 / Resolution: 1.893→17.409 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.06
RfactorNum. reflection% reflection
Rfree0.2279 899 10.72 %
Rwork0.1764 --
obs0.1818 4584 90.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.46 Å2 / Biso mean: 16.1865 Å2 / Biso min: 3.83 Å2
Refinement stepCycle: final / Resolution: 1.893→17.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms544 0 0 76 620
Biso mean---24.88 -
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 (%)
1.8934-2.01180.32421210.2255107976
2.0118-2.16690.26271480.1959116684
2.1669-2.38450.21631450.1711118088
2.3845-2.72840.25891560.1675134397
2.7284-3.43310.20671540.1699135799
3.4331-17.4090.19861750.16831366100

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