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- PDB-6q22: Coiled-coil Trimer with Glu:Aminobutyric acid:Lys Triad -

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Basic information

Entry
Database: PDB / ID: 6q22
TitleCoiled-coil Trimer with Glu:Aminobutyric acid:Lys Triad
ComponentsCoiled-coil Trimer with Glu:Aminobutyric acid:Lys Triad
KeywordsDE NOVO PROTEIN / Trimer / Helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.599 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 1.2Apr 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:Aminobutyric acid:Lys Triad
B: Coiled-coil Trimer with Glu:Aminobutyric acid:Lys Triad
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3925
Polymers7,6772
Non-polymers7153
Water95553
1
A: Coiled-coil Trimer with Glu:Aminobutyric acid:Lys Triad
hetero molecules

A: Coiled-coil Trimer with Glu:Aminobutyric acid:Lys Triad
hetero molecules

A: Coiled-coil Trimer with Glu:Aminobutyric acid:Lys Triad
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9459
Polymers11,5153
Non-polymers1,4306
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 area4950 Å2
ΔGint-25 kcal/mol
Surface area6960 Å2
MethodPISA
2
B: Coiled-coil Trimer with Glu:Aminobutyric acid:Lys Triad
hetero molecules

B: Coiled-coil Trimer with Glu:Aminobutyric acid:Lys Triad
hetero molecules

B: Coiled-coil Trimer with Glu:Aminobutyric acid:Lys Triad
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2306
Polymers11,5153
Non-polymers7153
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 area5240 Å2
ΔGint-35 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.364, 39.364, 98.120
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:Aminobutyric acid:Lys Triad


Mass: 3838.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.91 Å3/Da / Density % sol: 35.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 50% PEG400, 100 mM CHES/NaOH, pH 9.5, 200 mM sodium chloride

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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 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.599→32.71 Å / Num. obs: 7484 / % possible obs: 99.9 % / Redundancy: 3.6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.046 / Rrim(I) all: 0.104 / Net I/σ(I): 16.3
Reflection shellResolution: 1.599→1.656 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 748 / CC1/2: 0.837 / Rpim(I) all: 0.233 / Rrim(I) all: 0.369

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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: 1.599→32.71 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.46
RfactorNum. reflection% reflection
Rfree0.2141 1285 10.06 %
Rwork0.1913 --
obs0.1939 7484 85.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.84 Å2 / Biso mean: 20.2278 Å2 / Biso min: 7.58 Å2
Refinement stepCycle: final / Resolution: 1.599→32.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms540 0 45 53 638
Biso mean--35.49 29.24 -
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 (%)
1.599-1.66290.19071160.2023114375
1.6629-1.73850.23861290.2109114977
1.7385-1.83010.30691340.2214118080
1.8301-1.94460.24071440.1863122982
1.9446-2.09450.20251160.1741131184
2.0945-2.30480.1931440.1714132888
2.3048-2.63720.2171630.184136791
2.6372-3.31840.24181810.203137293
3.3184-16.860.18791580.1932141094

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