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- PDB-6os8: Coiled-coil Trimer with Glu:p-fluorophenylalanine:Lys Triad -

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Basic information

Entry
Database: PDB / ID: 6os8
TitleCoiled-coil Trimer with Glu:p-fluorophenylalanine:Lys Triad
ComponentsCoiled-coil trimer with Glu:p-fluorophenylalanine:Lys Triad
KeywordsDE NOVO PROTEIN / Trimer / Helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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
DepositionMay 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coiled-coil trimer with Glu:p-fluorophenylalanine:Lys Triad
B: Coiled-coil trimer with Glu:p-fluorophenylalanine:Lys Triad


Theoretical massNumber of molelcules
Total (without water)7,4082
Polymers7,4082
Non-polymers00
Water75742
1
A: Coiled-coil trimer with Glu:p-fluorophenylalanine:Lys Triad

A: Coiled-coil trimer with Glu:p-fluorophenylalanine:Lys Triad

A: Coiled-coil trimer with Glu:p-fluorophenylalanine:Lys Triad


Theoretical massNumber of molelcules
Total (without water)11,1133
Polymers11,1133
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 area3750 Å2
ΔGint-31 kcal/mol
Surface area6490 Å2
MethodPISA
2
B: Coiled-coil trimer with Glu:p-fluorophenylalanine:Lys Triad

B: Coiled-coil trimer with Glu:p-fluorophenylalanine:Lys Triad

B: Coiled-coil trimer with Glu:p-fluorophenylalanine:Lys Triad


Theoretical massNumber of molelcules
Total (without water)11,1133
Polymers11,1133
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-35 kcal/mol
Surface area6500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.066, 39.066, 98.623
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:p-fluorophenylalanine:Lys Triad


Mass: 3704.220 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.: 42 / Source method: isolated from a natural source / Formula: H2O

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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: 1.95 Å3/Da / Density % sol: 37.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 40% PEG300, 100 mM sodium cacodylate/HCl, pH 6.5, 200 mM calcium acetate

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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: Oct 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.15→19.93 Å / Num. obs: 3077 / % possible obs: 99.7 % / Redundancy: 4.1 % / CC1/2: 0.972 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.083 / Rrim(I) all: 0.184 / Net I/σ(I): 7.4
Reflection shellResolution: 2.15→2.227 Å / Rmerge(I) obs: 0.353 / Num. unique obs: 321 / CC1/2: 0.845 / Rpim(I) all: 0.282 / Rrim(I) all: 0.454 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_2906refinement
PDB_EXTRACT3.24data extraction
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UXT

5uxt


Resolution: 2.15→19.926 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 30.91
RfactorNum. reflection% reflection
Rfree0.2783 517 9.3 %
Rwork0.2 --
obs0.2071 3077 90.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.65 Å2 / Biso mean: 26.7169 Å2 / Biso min: 13.81 Å2
Refinement stepCycle: final / Resolution: 2.15→19.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms522 0 0 42 564
Biso mean---33.62 -
Num. residues----64
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1505-2.36660.31861110.22351158126982
2.3666-2.70830.33391390.21761222136189
2.7083-3.40940.30461230.20821287141092
3.4094-19.92670.23951440.18361375151999

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