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- PDB-7q1r: A de novo designed homo-dimeric antiparallel coiled coil apCC-Di -

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Basic information

Entry
Database: PDB / ID: 7q1r
TitleA de novo designed homo-dimeric antiparallel coiled coil apCC-Di
ComponentsapCC-Di
KeywordsDE NOVO PROTEIN / antiparallel / homo-dimeric / coiled-coil / de novo / protein design / associating peptides
Function / homologyETHANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsShanmugaratnam, S. / Rhys, G.G. / Dawson, W.M. / Woolfson, D.N. / Hocker, B.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission888993European Union
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: De novo designed peptides for cellular delivery and subcellular localisation.
Authors: Rhys, G.G. / Cross, J.A. / Dawson, W.M. / Thompson, H.F. / Shanmugaratnam, S. / Savery, N.J. / Dodding, M.P. / Hocker, B. / Woolfson, D.N.
History
DepositionOct 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 31, 2022Group: 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 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: apCC-Di
B: apCC-Di
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8774
Polymers6,8082
Non-polymers692
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-21 kcal/mol
Surface area4850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.096, 35.096, 92.433
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-101-

EOH

21A-201-

HOH

31B-231-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 4 or resid 7 through 10 or resid 12 or resid 14 through 31))
d_2ens_1(chain "B" and (resid 1 through 4 or resid 7 through 10 or resid 12 or resid 14 through 31))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYGLUA1 - 4
d_12ens_1LEULEUA7 - 10
d_13ens_1GLNGLNA12
d_14ens_1ILEGLYA14 - 30
d_21ens_1GLYGLUE2 - 5
d_22ens_1LEULEUE8 - 11
d_23ens_1GLNGLNE13
d_24ens_1ILEGLYE15 - 31

NCS oper: (Code: givenMatrix: (0.987687711141, -0.153601000311, 0.0296600398479), (-0.153557789067, -0.988132580609, -0.00374280043753), (0.0298829496071, -0.000857812145288, -0.999553036853)Vector: - ...NCS oper: (Code: given
Matrix: (0.987687711141, -0.153601000311, 0.0296600398479), (-0.153557789067, -0.988132580609, -0.00374280043753), (0.0298829496071, -0.000857812145288, -0.999553036853)
Vector: -0.286868951925, 2.78972688728, 18.742491002)

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Components

#1: Protein/peptide apCC-Di


Mass: 3403.910 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% ethanol, 1.5 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.08→27.95 Å / Num. obs: 25670 / % possible obs: 99.6 % / Redundancy: 10.6 % / Biso Wilson estimate: 14.52 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.033 / Rrim(I) all: 0.111 / Net I/σ(I): 64.93
Reflection shellResolution: 1.08→1.12 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.612 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 2505 / CC1/2: 0.33 / CC star: 0.705 / Rpim(I) all: 0.533 / Rrim(I) all: 1.701 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALS2.0.2data reduction
DIALS2.0.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: poly-alanine coiled-coil

Resolution: 1.08→27.95 Å / SU ML: 0.1326 / Cross valid method: FREE R-VALUE / Phase error: 24.3192
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2168 1283 5.01 %
Rwork0.1892 24313 -
obs0.1906 25596 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.18 Å2
Refinement stepCycle: LAST / Resolution: 1.08→27.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms474 0 9 93 576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0105511
X-RAY DIFFRACTIONf_angle_d0.9428688
X-RAY DIFFRACTIONf_chiral_restr0.059974
X-RAY DIFFRACTIONf_plane_restr0.009694
X-RAY DIFFRACTIONf_dihedral_angle_d20.3522204
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.04734470194 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.120.34821390.34832638X-RAY DIFFRACTION99.46
1.12-1.170.2851400.27832621X-RAY DIFFRACTION99.07
1.17-1.240.26061390.2622637X-RAY DIFFRACTION99.28
1.24-1.310.25111390.24182659X-RAY DIFFRACTION99.89
1.31-1.420.26411420.22652682X-RAY DIFFRACTION99.86
1.42-1.560.22011400.19342665X-RAY DIFFRACTION99.26
1.56-1.780.19291450.18082731X-RAY DIFFRACTION99.86
1.78-2.250.19081450.1742751X-RAY DIFFRACTION99.9
2.25-27.950.21121540.17182929X-RAY DIFFRACTION99.84
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)
10.9394789352030.2125289620110.4806428327741.70042190421-0.7061207695680.809584217665-0.09889537017420.0112540833893-0.04216945369380.0914397751191-0.0087005286388-0.008193777641070.186015047425-0.101821228246-0.003723456371470.0632048367615-0.0110093974057-0.003122829318910.08655998633520.006630218256230.09953435383710.9836332776-3.3166993899310.8476569944
20.769133621976-0.3059215165470.1405229224291.45538444998-0.05792998587482.50399734668-0.0290739774301-0.03606254611690.00777610116826-0.0589680368450.0682772961046-0.0776219574224-0.172783105251-0.1397286772920.05966374643960.08824518109520.01184902986570.003670950226460.125732426995-2.94557878772E-50.13280938674611.26590320144.292474135857.63809284874
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 1 through 31)AA - B1 - 311
22(chain 'B' and resid 0 through 31)BD - F0 - 31

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