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- PDB-6ov9: Coiled-coil Trimer with Glu:p-nitrophenylalanine:Lys Triad -

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Basic information

Entry
Database: PDB / ID: 6ov9
TitleCoiled-coil Trimer with Glu:p-nitrophenylalanine:Lys Triad
ComponentsCoiled-coil Trimer with Glu:p-nitrophenylalanine:Lys Triad
KeywordsDE NOVO PROTEIN / Trimer / Helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 7, 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 1.2Apr 2, 2025Group: 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:p-nitrophenylalanine:Lys Triad
B: Coiled-coil Trimer with Glu:p-nitrophenylalanine:Lys Triad


Theoretical massNumber of molelcules
Total (without water)7,8912
Polymers7,8912
Non-polymers00
Water54030
1
A: Coiled-coil Trimer with Glu:p-nitrophenylalanine:Lys Triad

A: Coiled-coil Trimer with Glu:p-nitrophenylalanine:Lys Triad

A: Coiled-coil Trimer with Glu:p-nitrophenylalanine:Lys Triad


Theoretical massNumber of molelcules
Total (without water)11,8363
Polymers11,8363
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 area6670 Å2
MethodPISA
2
B: Coiled-coil Trimer with Glu:p-nitrophenylalanine:Lys Triad

B: Coiled-coil Trimer with Glu:p-nitrophenylalanine:Lys Triad

B: Coiled-coil Trimer with Glu:p-nitrophenylalanine:Lys Triad


Theoretical massNumber of molelcules
Total (without water)11,8363
Polymers11,8363
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 area3710 Å2
ΔGint-34 kcal/mol
Surface area6780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.051, 39.051, 101.173
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-nitrophenylalanine:Lys Triad


Mass: 3945.472 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.: 30 / 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: 1.79 Å3/Da / Density % sol: 31.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 40% PEG300, 100 mM sodium phosphate dibasic/citric acid, pH 4.2

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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: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.1→16.9 Å / Num. obs: 7199 / % possible obs: 99.76 % / Redundancy: 10.9 % / CC1/2: 0.903 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.062 / Rrim(I) all: 0.229 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.626 / Num. unique obs: 333 / CC1/2: 0.841 / Rpim(I) all: 0.272 / Rrim(I) all: 0.684 / % possible all: 100

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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: 2.1→16.898 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 30.97
RfactorNum. reflection% reflection
Rfree0.2701 710 10.63 %
Rwork0.2095 --
obs0.2162 6678 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 49.4 Å2 / Biso mean: 27.5204 Å2 / Biso min: 11.66 Å2
Refinement stepCycle: final / Resolution: 2.1→16.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms556 0 0 30 586
Biso mean---31.05 -
Num. residues----68
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 (%)
2.1001-2.26190.27811390.20951183132298
2.2619-2.48890.27491280.19981173130199
2.4889-2.84760.26351660.213712001366100
2.8476-3.5820.30061200.198412241344100
3.582-16.89820.25421570.218611881345100

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