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- PDB-8b45: Structure of CC-Tri with Aib@b,c: CC-Tri-(UbUc)4 -

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Basic information

Entry
Database: PDB / ID: 8b45
TitleStructure of CC-Tri with Aib@b,c: CC-Tri-(UbUc)4
ComponentsCC-Tri-(UbUc)4
KeywordsDE NOVO PROTEIN / aib / coiled coil / trimer / 2-Aminoisobutyric acid
Function / homologyTRIETHYLENE GLYCOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.6 Å
AuthorsKumar, P. / Martin, F.J.O. / Dawson, W.M. / Zieleniewski, F. / Woolfson, D.N.
Funding supportEuropean Union, United Kingdom, 4items
OrganizationGrant numberCountry
European Research Council (ERC)340764European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/G036764 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00661X/1 United Kingdom
CitationJournal: To Be Published
Title: Structure of CC-Tri with Aib@b,c: CC-Tri-(UbUc)4
Authors: Kumar, P. / Martin, F.J.O. / Dawson, W.M. / Zieleniewski, F. / Woolfson, D.N.
History
DepositionSep 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: CC-Tri-(UbUc)4
C: CC-Tri-(UbUc)4
D: CC-Tri-(UbUc)4
A: CC-Tri-(UbUc)4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,87618
Polymers13,3884
Non-polymers48814
Water79344
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-167 kcal/mol
Surface area7230 Å2
Unit cell
Length a, b, c (Å)85.515, 85.515, 85.515
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-208-

HOH

21A-209-

HOH

31A-211-

HOH

41A-213-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
12B
22D
13B
23A
14C
24D
15C
25A
16D
26A

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYBA1 - 302 - 31
21GLYGLYCB1 - 302 - 31
12GLYGLYBA1 - 302 - 31
22GLYGLYDC1 - 302 - 31
13ILEILEBA1 - 272 - 28
23ILEILEAD1 - 272 - 28
14GLYGLYCB1 - 302 - 31
24GLYGLYDC1 - 302 - 31
15ILEILECB1 - 272 - 28
25ILEILEAD1 - 272 - 28
16ILEILEDC1 - 272 - 28
26ILEILEAD1 - 272 - 28

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein/peptide
CC-Tri-(UbUc)4


Mass: 3347.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 36.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8 M Potasium sodium tartrate tetrahydrate 0.1 M Sodium HEPES 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.6→60.47 Å / Num. obs: 13883 / % possible obs: 100 % / Redundancy: 33.9 % / CC1/2: 1 / Net I/σ(I): 30.2
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 670 / CC1/2: 1

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.6→60.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.197 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1337 9.6 %RANDOM
Rwork0.1863 ---
obs0.1889 12545 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.54 Å2 / Biso mean: 32.193 Å2 / Biso min: 17.15 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.6→60.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 26 44 998
Biso mean--46.99 42.41 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013947
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171084
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.6511310
X-RAY DIFFRACTIONr_angle_other_deg1.1781.5782449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.845116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51226.16730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43415195
X-RAY DIFFRACTIONr_chiral_restr0.0930.2113
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02964
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02156
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B8360.12
12C8360.12
21B8500.14
22D8500.14
31B7480.15
32A7480.15
41C8350.14
42D8350.14
51C7380.16
52A7380.16
61D7500.16
62A7500.16
LS refinement shellResolution: 1.601→1.647 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.278 103 -
Rwork0.282 931 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
112.1797-2.4623-4.93092.02841.36774.4288-0.0614-0.19990.02350.0682-0.01290.03820.03020.00710.07430.0495-0.0112-0.02160.01670.01020.024964.406914.8701-9.3027
27.8132-0.4922-0.87510.75040.16070.77370.03480.0418-0.0119-0.0339-0.01190.01160.0333-0.0121-0.02290.1076-0.0069-0.00040.07550.00540.049263.31796.2911-4.1158
311.373-5.2132-7.42665.62794.51668.64110.03410.056-0.0117-0.0138-0.0866-0.1885-0.08550.06680.05250.0239-0.0013-0.01420.0060.00720.021665.376420.6781-15.1384
46.8032-2.6564-0.71641.69370.21740.67360.08810.1074-0.0286-0.0865-0.0484-0.02410.01150.0019-0.03970.1051-0.0151-0.0140.1061-0.00490.083759.68446.8032-13.6124
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B0 - 31
2X-RAY DIFFRACTION2C1 - 30
3X-RAY DIFFRACTION3D0 - 30
4X-RAY DIFFRACTION4A0 - 28

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