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- PDB-8a3j: X-ray crystal structure of a de novo designed antiparallel coiled... -

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Basic information

Entry
Database: PDB / ID: 8a3j
TitleX-ray crystal structure of a de novo designed antiparallel coiled-coil heterotetramer with 3 heptad repeats, apCC-Tet*3-A2B2
Components
  • apCC-Tet*3-A
  • apCC-Tet*3-B
KeywordsDE NOVO PROTEIN / coiled coil / 4-helix bundle / de novo protein design / peptide assembly
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.1 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 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _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: apCC-Tet*3-A
B: apCC-Tet*3-B
C: apCC-Tet*3-A
D: apCC-Tet*3-B
E: apCC-Tet*3-A
F: apCC-Tet*3-B
G: apCC-Tet*3-A
H: apCC-Tet*3-B


Theoretical massNumber of molelcules
Total (without water)21,1178
Polymers21,1178
Non-polymers00
Water43224
1
A: apCC-Tet*3-A
B: apCC-Tet*3-B
C: apCC-Tet*3-A
D: apCC-Tet*3-B


Theoretical massNumber of molelcules
Total (without water)10,5584
Polymers10,5584
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-45 kcal/mol
Surface area5270 Å2
MethodPISA
2
E: apCC-Tet*3-A
F: apCC-Tet*3-B
G: apCC-Tet*3-A
H: apCC-Tet*3-B


Theoretical massNumber of molelcules
Total (without water)10,5584
Polymers10,5584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-42 kcal/mol
Surface area4880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.660, 63.160, 47.301
Angle α, β, γ (deg.)90.000, 91.680, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide
apCC-Tet*3-A


Mass: 2650.932 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide
apCC-Tet*3-B


Mass: 2628.292 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.8 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: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→37.85 Å / Num. obs: 9443 / % possible obs: 98.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 22.57 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.103 / Rrim(I) all: 0.27 / Net I/σ(I): 4.8 / Num. measured all: 64760 / Scaling rejects: 283
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.1671.153827680.8060.4441.1871.798.2
8.91-37.856.20.1038091310.9910.0440.1129.397.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.1→37.85 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2692 389 4.13 %
Rwork0.2272 9025 -
obs0.2288 9414 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.84 Å2 / Biso mean: 29.3805 Å2 / Biso min: 14.41 Å2
Refinement stepCycle: final / Resolution: 2.1→37.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1275 0 0 24 1299
Biso mean---33.9 -
Num. residues----186
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 (%)
2.1-2.40.3211180.25172975309398
2.4-3.030.28071480.24642982313098
3.03-37.850.24421230.21033068319199
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)
12.55630.7654-0.25543.8591-0.37831.390.0547-0.08750.0111-0.0234-0.1027-0.258-0.0124-0.02580.05590.11180.0324-0.03860.1669-0.02120.1438-15.2467-15.5953-0.1911
21.5211-0.6401-0.00952.29850.36931.98860.03710.13670.0734-0.10670.00870.03850.1149-0.0249-0.03480.2137-0.0106-0.00650.26630.00330.1857-2.6829-7.8876-22.9004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' or chain 'C' or chain 'D' or chain 'A'B0 - 24
2X-RAY DIFFRACTION1chain 'B' or chain 'C' or chain 'D' or chain 'A'C0 - 24
3X-RAY DIFFRACTION1chain 'B' or chain 'C' or chain 'D' or chain 'A'D0 - 22
4X-RAY DIFFRACTION1chain 'B' or chain 'C' or chain 'D' or chain 'A'A0 - 24
5X-RAY DIFFRACTION2chain 'G' or chain 'E' or chain 'H' or chain 'F'G2 - 24
6X-RAY DIFFRACTION2chain 'G' or chain 'E' or chain 'H' or chain 'F'E2 - 22
7X-RAY DIFFRACTION2chain 'G' or chain 'E' or chain 'H' or chain 'F'H1 - 22
8X-RAY DIFFRACTION2chain 'G' or chain 'E' or chain 'H' or chain 'F'F1 - 22

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