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- PDB-5uxt: Coiled-coil Trimer with Glu:Trp:Lys Triad -

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Basic information

Entry
Database: PDB / ID: 5uxt
TitleCoiled-coil Trimer with Glu:Trp:Lys Triad
Componentscoiled-coil trimer with Glu:Trp:Lys triad
KeywordsDE NOVO PROTEIN / Coiled coil / Triad
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2.197 Å
AuthorsSmith, M.S. / Billings, W.M. / Whitby, F.G. / Miller, M.B. / Price, J.L.
CitationJournal: Org. Biomol. Chem. / Year: 2017
Title: Enhancing a long-range salt bridge with intermediate aromatic and nonpolar amino acids.
Authors: Smith, M.S. / Billings, W.M. / Whitby, F.G. / Miller, M.B. / Price, J.L.
History
DepositionFeb 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: coiled-coil trimer with Glu:Trp:Lys triad
B: coiled-coil trimer with Glu:Trp:Lys triad
C: coiled-coil trimer with Glu:Trp:Lys triad
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9114
Polymers11,8193
Non-polymers921
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-31 kcal/mol
Surface area6620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.815, 38.516, 37.031
Angle α, β, γ (deg.)90.000, 113.340, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide coiled-coil trimer with Glu:Trp:Lys triad


Mass: 3939.510 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.3 uL protein + 0.3 uL 50% v/v PEG200, 0.1 M sodium/potassium phosphate, pH 6.2, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.197→40 Å / Num. obs: 5259 / % possible obs: 92 % / Redundancy: 3.9 % / Biso Wilson estimate: 30.93 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.073 / Rrim(I) all: 0.153 / Χ2: 1.127 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.282.30.3930.8220.2650.4771.31562.7
2.28-2.372.70.5020.7560.3180.5981.12473.7
2.37-2.483.10.4780.8070.2810.5581.10387.5
2.48-2.613.60.4520.8680.250.5190.99496.1
2.61-2.7740.3290.9060.1820.3791.15599.5
2.77-2.994.40.2790.9470.1490.3181.069100
2.99-3.294.60.2280.950.1220.261.126100
3.29-3.764.60.1080.9910.0580.1231.074100
3.76-4.744.60.0770.9940.040.0871.229100
4.74-404.40.0790.9970.0430.0911.17399.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.197→22.342 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.44
RfactorNum. reflection% reflection
Rfree0.2745 529 10.06 %
Rwork0.1938 --
obs0.2024 5256 91.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.99 Å2 / Biso mean: 44.9394 Å2 / Biso min: 19.16 Å2
Refinement stepCycle: final / Resolution: 2.197→22.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms782 0 14 57 853
Biso mean--77.4 46.33 -
Num. residues----96
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007797
X-RAY DIFFRACTIONf_angle_d0.8381061
X-RAY DIFFRACTIONf_chiral_restr0.038113
X-RAY DIFFRACTIONf_plane_restr0.004131
X-RAY DIFFRACTIONf_dihedral_angle_d25.037490
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 (%)
2.1968-2.41770.3367960.2392910100671
2.4177-2.76690.32391390.23821226136596
2.7669-3.48390.29441510.197212681419100
3.4839-22.34290.24071430.170213231466100
Refinement TLS params.Method: refined / Origin x: 21.336 Å / Origin y: -0.703 Å / Origin z: 8.6277 Å
111213212223313233
T0.2594 Å2-0.0177 Å20.0559 Å2-0.1596 Å2-0.023 Å2--0.3211 Å2
L3.0068 °2-0.3353 °2-0.4453 °2-2.8057 °2-0.1996 °2--1.7198 °2
S0.106 Å °0.1863 Å °-0.0685 Å °-0.0641 Å °-0.0749 Å °-0.0598 Å °-0.0195 Å °0.0495 Å °-0.02 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 33
2X-RAY DIFFRACTION1allB0 - 29
3X-RAY DIFFRACTION1allC0 - 31
4X-RAY DIFFRACTION1allS1 - 77
5X-RAY DIFFRACTION1allG1

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