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- PDB-7bo8: A hexameric de novo coiled-coil assembly: CC-Type2-(VaYd)4-Y3F-W1... -

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Basic information

Entry
Database: PDB / ID: 7bo8
TitleA hexameric de novo coiled-coil assembly: CC-Type2-(VaYd)4-Y3F-W19(BrPhe)-Y24F.
ComponentsCC-Type2-(VaYd)4-Y3F-W19(BrPhe)-Y24F
KeywordsDE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly / tyrosine-tyrosine interactions
Function / homologyOXAMIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.84 Å
AuthorsRhys, G.G. / Brady, R.L. / Woolfson, D.N.
Funding supportEuropean Union, United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council (ERC)340764European Union
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
CitationJournal: Biomacromolecules / Year: 2021
Title: How Coiled-Coil Assemblies Accommodate Multiple Aromatic Residues.
Authors: Rhys, G.G. / Dawson, W.M. / Beesley, J.L. / Martin, F.J.O. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N.
History
DepositionJan 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 9, 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

Downloads & links

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Assembly

Deposited unit
A: CC-Type2-(VaYd)4-Y3F-W19(BrPhe)-Y24F
B: CC-Type2-(VaYd)4-Y3F-W19(BrPhe)-Y24F
C: CC-Type2-(VaYd)4-Y3F-W19(BrPhe)-Y24F
D: CC-Type2-(VaYd)4-Y3F-W19(BrPhe)-Y24F
E: CC-Type2-(VaYd)4-Y3F-W19(BrPhe)-Y24F
F: CC-Type2-(VaYd)4-Y3F-W19(BrPhe)-Y24F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4718
Polymers20,3206
Non-polymers1512
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10140 Å2
ΔGint-89 kcal/mol
Surface area9660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.150, 53.250, 111.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
CC-Type2-(VaYd)4-Y3F-W19(BrPhe)-Y24F


Mass: 3386.687 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: After 1:1 dilution with the peptide solution the resulting conditions were 0.05 M Sodium formate, 0.05 M Ammonium acetate, 0.05 M Sodium citrate tribasic dihydrate, 0.05 M Potassium sodium ...Details: After 1:1 dilution with the peptide solution the resulting conditions were 0.05 M Sodium formate, 0.05 M Ammonium acetate, 0.05 M Sodium citrate tribasic dihydrate, 0.05 M Potassium sodium tartrate tetrahydrate, 0.05 M Sodium oxamate, 0.05 M Tris, 0.05 M BICINE, 6% v/v Ethylene glycol and 3% w/v PEG 8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91983 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91983 Å / Relative weight: 1
ReflectionResolution: 1.84→38.57 Å / Num. obs: 16884 / % possible obs: 99.9 % / Redundancy: 32.1 % / Biso Wilson estimate: 45.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.03 / Rrim(I) all: 0.176 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) all% possible all
1.84-1.89132.2090.811990.610.8610.6322.299100
8.23-38.57280.11329.22370.9970.0210.11597.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSJun 1, 2017data reduction
XSCALEJun 1, 2017data scaling
xia20.5.438-g5f426072-dials-1.7data scaling
CRANK2phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.84→38.57 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.208 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2665 824 4.9 %RANDOM
Rwork0.2009 ---
obs0.204 16006 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.15 Å2 / Biso mean: 47.797 Å2 / Biso min: 32.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20 Å2
2--1.04 Å20 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 1.84→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 10 32 1457
Biso mean--61.52 48.45 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131457
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181402
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.6661907
X-RAY DIFFRACTIONr_angle_other_deg1.3471.6073235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1965164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36524.25467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70215242
X-RAY DIFFRACTIONr_chiral_restr0.0790.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021583
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02301
LS refinement shellResolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 48 -
Rwork0.321 1145 -
all-1193 -
obs--99.83 %

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