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- PDB-6xy0: Crystal structure of a de novo designed parallel four-helix coile... -

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Basic information

Entry
Database: PDB / ID: 6xy0
TitleCrystal structure of a de novo designed parallel four-helix coiled coil, 3-EK-4
Components3-EK-4
KeywordsDE NOVO PROTEIN / coiled coil / tetramer / parallel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å
AuthorsEdgell, C.L. / Savery, N.J. / Woolfson, D.N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S002820/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)EP/L016494/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/L016494/1 United Kingdom
CitationJournal: Biochemistry / Year: 2020
Title: RobustDe Novo-Designed Homotetrameric Coiled Coils.
Authors: Edgell, C.L. / Savery, N.J. / Woolfson, D.N.
History
DepositionJan 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-EK-4
B: 3-EK-4
C: 3-EK-4
D: 3-EK-4


Theoretical massNumber of molelcules
Total (without water)13,8484
Polymers13,8484
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-51 kcal/mol
Surface area7460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.460, 48.550, 36.570
Angle α, β, γ (deg.)90.000, 96.190, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide
3-EK-4


Mass: 3462.024 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.88 Å3/Da / Density % sol: 34.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M sodium HEPES, 0.2 sodium citrate tribasic dihydrate, 20 % 2-propanol, pH 7.5, supplemented with 25% glycerol for cryo-protection

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.11→48.55 Å / Num. obs: 38599 / % possible obs: 94.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 12.88 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.7
Reflection shellResolution: 1.11→1.12 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1806 / CC1/2: 0.629 / % possible all: 90.6

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Processing

Software
NameVersionClassification
PHENIX1.16-3546refinement
iMOSFLM7.2.2data reduction
Aimlessdata scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.11→29.29 Å / SU ML: 0.1159 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.8101
RfactorNum. reflection% reflection
Rfree0.1994 3797 9.85 %
Rwork0.1639 --
obs0.1674 38546 94.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.42 Å2
Refinement stepCycle: LAST / Resolution: 1.11→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 0 134 1111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451023
X-RAY DIFFRACTIONf_angle_d0.61781372
X-RAY DIFFRACTIONf_chiral_restr0.0439150
X-RAY DIFFRACTIONf_plane_restr0.0026181
X-RAY DIFFRACTIONf_dihedral_angle_d9.9085672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.11-1.120.3211460.31041212X-RAY DIFFRACTION90.53
1.12-1.130.26941340.27891253X-RAY DIFFRACTION90.01
1.13-1.150.27771250.25041217X-RAY DIFFRACTION90.92
1.15-1.170.27781350.24221224X-RAY DIFFRACTION90.54
1.17-1.180.26211470.23471273X-RAY DIFFRACTION92.09
1.18-1.20.26381340.21061195X-RAY DIFFRACTION90.72
1.2-1.220.2381390.19571282X-RAY DIFFRACTION92.63
1.22-1.240.23561410.19491230X-RAY DIFFRACTION91.58
1.24-1.270.20521340.17951284X-RAY DIFFRACTION92.62
1.27-1.290.2111370.15861259X-RAY DIFFRACTION93.32
1.29-1.320.22671400.15991269X-RAY DIFFRACTION93.13
1.32-1.350.20061330.16111288X-RAY DIFFRACTION93.43
1.35-1.380.17511120.1591275X-RAY DIFFRACTION93.84
1.38-1.410.17111410.15251326X-RAY DIFFRACTION94.46
1.41-1.450.20111440.14691248X-RAY DIFFRACTION94.25
1.45-1.490.17041570.14451286X-RAY DIFFRACTION94.62
1.49-1.540.18561350.13561302X-RAY DIFFRACTION94.85
1.54-1.60.16231470.13151298X-RAY DIFFRACTION95.25
1.6-1.660.16761480.13561290X-RAY DIFFRACTION95.55
1.66-1.730.21191430.14571344X-RAY DIFFRACTION96.31
1.73-1.830.18711460.15051310X-RAY DIFFRACTION96.42
1.83-1.940.18181640.15621306X-RAY DIFFRACTION96.46
1.94-2.090.1981470.15681319X-RAY DIFFRACTION97.28
2.09-2.30.20981320.15551347X-RAY DIFFRACTION97.3
2.3-2.630.18611620.16011334X-RAY DIFFRACTION97.52
2.63-3.320.20561320.1631378X-RAY DIFFRACTION98.37
3.32-29.290.19791420.17221400X-RAY DIFFRACTION98.66

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