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- PDB-8a3i: X-ray crystal structure of a de novo designed antiparallel coiled... -

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Basic information

Entry
Database: PDB / ID: 8a3i
TitleX-ray crystal structure of a de novo designed antiparallel coiled-coil homotetramer with 3 heptad repeats, apCC-Tet*3
ComponentsapCC-Tet*3
KeywordsDE NOVO PROTEIN / coiled coil / 4-helix bundle / de novo protein design / peptide assembly
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsNaudin, E.A. / Mylemans, B. / Albanese, K.I. / Woolfson, D.N.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S002820/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006231/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V004220/1 United Kingdom
Max Planck Bristol Centre for Minimal Biology - University of Bristol United Kingdom
CitationJournal: Chem Sci / Year: 2022
Title: From peptides to proteins: coiled-coil tetramers to single-chain 4-helix bundles.
Authors: Naudin, E.A. / Albanese, K.I. / Smith, A.J. / Mylemans, B. / Baker, E.G. / Weiner, O.D. / Andrews, D.M. / Tigue, N. / Savery, N.J. / Woolfson, D.N.
History
DepositionJun 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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: apCC-Tet*3
B: apCC-Tet*3


Theoretical massNumber of molelcules
Total (without water)5,2982
Polymers5,2982
Non-polymers00
Water1629
1
A: apCC-Tet*3
B: apCC-Tet*3

A: apCC-Tet*3
B: apCC-Tet*3


Theoretical massNumber of molelcules
Total (without water)10,5964
Polymers10,5964
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4740 Å2
ΔGint-50 kcal/mol
Surface area5600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.028, 49.028, 32.618
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein/peptide apCC-Tet*3


Mass: 2649.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.4 M sodium citrate tribasic dihydrate 0.1 M sodium HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9253 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9253 Å / Relative weight: 1
ReflectionResolution: 1.4→42.46 Å / Num. obs: 8997 / % possible obs: 98.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 16.64 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.021 / Rrim(I) all: 0.038 / Net I/σ(I): 15.2 / Num. measured all: 27514 / Scaling rejects: 1221
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.7 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.420.39611434290.5050.2990.5011.795.9
7.67-42.460.047191700.9690.0390.06138.196.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold model

Resolution: 1.42→42.46 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 425 4.95 %
Rwork0.1995 8161 -
obs0.2014 8586 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.16 Å2 / Biso mean: 28.423 Å2 / Biso min: 12.22 Å2
Refinement stepCycle: final / Resolution: 1.42→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms352 0 0 9 361
Biso mean---38.03 -
Num. residues----50
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.42-1.630.3021410.22022638277996
1.63-2.050.23591000.22562754285498
2.05-42.460.22351840.18872769295398

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