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- PDB-7q1q: De novo designed homo-dimeric antiparallel helices Homomer-S -

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Basic information

Entry
Database: PDB / ID: 7q1q
TitleDe novo designed homo-dimeric antiparallel helices Homomer-S
ComponentsHomomer-S
KeywordsDE NOVO PROTEIN / antiparallel homo-dimeric coiled-coil / de novo / protein design / associating peptides
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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 / Structure summary / Category: citation / citation_author / struct
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _struct.title
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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homomer-S
B: Homomer-S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7253
Polymers6,6662
Non-polymers591
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-12 kcal/mol
Surface area5550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)19.581, 21.421, 25.769
Angle α, β, γ (deg.)94.880, 91.550, 97.870
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide Homomer-S


Mass: 3332.809 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.6 Å3/Da / Density % sol: 23.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1 M Acetate pH 6.5, 0.1 M imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 7, 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→17.08 Å / Num. obs: 20583 / % possible obs: 92.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 10.6 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.026 / Rrim(I) all: 0.049 / Net I/σ(I): 12.69
Reflection shellResolution: 1→1.04 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.351 / Mean I/σ(I) obs: 0.81 / Num. unique obs: 1960 / CC1/2: 0.451 / CC star: 0.788 / Rpim(I) all: 0.848 / Rrim(I) all: 1.6 / % possible all: 87.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDS20200417data reduction
XDS20200417data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Poly-Alanine coiled-coil

Resolution: 1→17.08 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / Phase error: 28.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 1029 5 %
Rwork0.157 19561 -
obs0.16 20573 91.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 42.53 Å2 / Biso mean: 15.3 Å2 / Biso min: 7.32 Å2
Refinement stepCycle: final / Resolution: 1→17.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms471 0 7 63 541
Biso mean--32.04 25.17 -
Num. residues----63
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1-1.040.41441350.398256184
1.05-1.120.30541440.2585273389
1.12-1.20.24641450.193276091
1.2-1.320.2061480.1559281492
1.32-1.510.17651500.1332286193
1.52-1.910.15731530.1516288995
1.91-17.080.18341550.1378294397

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