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- PDB-6ovu: Coiled-coil Trimer with Glu:3,4-difluorophenylalanine:Lys Triad -

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Basic information

Entry
Database: PDB / ID: 6ovu
TitleCoiled-coil Trimer with Glu:3,4-difluorophenylalanine:Lys Triad
ComponentsCoiled-coil Trimer with Glu:3,4-difluorophenylalanine:Lys Triad
KeywordsDE NOVO PROTEIN / Trimer / Helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.101 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 8, 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 1.2Nov 20, 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:3,4-difluorophenylalanine:Lys Triad
B: Coiled-coil Trimer with Glu:3,4-difluorophenylalanine:Lys Triad


Theoretical massNumber of molelcules
Total (without water)7,8732
Polymers7,8732
Non-polymers00
Water61334
1
A: Coiled-coil Trimer with Glu:3,4-difluorophenylalanine:Lys Triad

A: Coiled-coil Trimer with Glu:3,4-difluorophenylalanine:Lys Triad

A: Coiled-coil Trimer with Glu:3,4-difluorophenylalanine:Lys Triad


Theoretical massNumber of molelcules
Total (without water)11,8093
Polymers11,8093
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 area3740 Å2
ΔGint-31 kcal/mol
Surface area6530 Å2
MethodPISA
2
B: Coiled-coil Trimer with Glu:3,4-difluorophenylalanine:Lys Triad

B: Coiled-coil Trimer with Glu:3,4-difluorophenylalanine:Lys Triad

B: Coiled-coil Trimer with Glu:3,4-difluorophenylalanine:Lys Triad


Theoretical massNumber of molelcules
Total (without water)11,8093
Polymers11,8093
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 area3760 Å2
ΔGint-35 kcal/mol
Surface area6670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.286, 39.286, 98.710
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-118-

HOH

21A-119-

HOH

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Components

#1: Protein/peptide Coiled-coil Trimer with Glu:3,4-difluorophenylalanine:Lys Triad


Mass: 3936.455 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.: 34 / 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: 35.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
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: Aug 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.101→16.45 Å / Num. obs: 3316 / % possible obs: 99.58 % / Redundancy: 4.6 % / CC1/2: 0.966 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.68 / Rrim(I) all: 0.168 / Net I/σ(I): 17.1
Reflection shellResolution: 2.101→2.176 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 2 / Num. unique obs: 334 / CC1/2: 0.72 / Rpim(I) all: 0.282 / Rrim(I) all: 0.483 / % possible all: 99.4

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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 / Resolution: 2.101→16.45 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.7
RfactorNum. reflection% reflection
Rfree0.2583 639 10.42 %
Rwork0.1906 --
obs0.1974 3316 92.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.79 Å2 / Biso mean: 28.5072 Å2 / Biso min: 13.38 Å2
Refinement stepCycle: final / Resolution: 2.101→16.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms539 0 0 34 573
Biso mean---32.67 -
Num. residues----66
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007545
X-RAY DIFFRACTIONf_angle_d0.791727
X-RAY DIFFRACTIONf_chiral_restr0.0377
X-RAY DIFFRACTIONf_plane_restr0.00391
X-RAY DIFFRACTIONf_dihedral_angle_d10.251333
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1013-2.26310.31741220.2325974109682
2.2631-2.49020.31511320.21331025115788
2.4902-2.8490.21851390.18951115125494
2.849-3.58370.25641340.18991185131999
3.5837-16.76470.24091120.174711961308100

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