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- PDB-9tlr: De novo designed single-chain antiparallel coiled-coil hairpin wi... -

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Basic information

Entry
Database: PDB / ID: 9tlr
TitleDe novo designed single-chain antiparallel coiled-coil hairpin with binding site for BCL-xL, Sc-apCC-2-BCL-xL-11
ComponentsSc-apCC-2-BCL-xL-11
KeywordsDE NOVO PROTEIN / Protein Binder / Computational Design / Coiled-coil
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMylemans, B. / Woolfson, D.N.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006231/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006703/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V008412/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V008412/2 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: De Novo-Designed Bifunctional
Authors: Mylemans, B. / Korona, B. / Acevedo-Jake, A.M. / MacRae, A. / Edwards, T.A. / Huang, D.T. / Wilson, A.J. / Itzhaki, L.S. / Woolfson, D.N.
History
DepositionDec 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sc-apCC-2-BCL-xL-11


Theoretical massNumber of molelcules
Total (without water)8,5641
Polymers8,5641
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.696, 58.696, 83.329
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-119-

HOH

21A-137-

HOH

31A-138-

HOH

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Components

#1: Protein Sc-apCC-2-BCL-xL-11


Mass: 8563.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1 M Sodium malonate dibasic monohydrate, 0.1 M HEPES, 0.5 % v/v Jeffamine ED-2003

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.62 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 1.95→29.4 Å / Num. obs: 5598 / % possible obs: 99.96 % / Redundancy: 23 % / Biso Wilson estimate: 31.36 Å2 / CC1/2: 1 / Net I/σ(I): 15.67
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 7468 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.4 Å / SU ML: 0.2489 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 19.7664
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2451 281 5.02 %
Rwork0.2202 5315 -
obs0.2216 5596 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.31 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms546 0 0 38 584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054552
X-RAY DIFFRACTIONf_angle_d0.8017746
X-RAY DIFFRACTIONf_chiral_restr0.042587
X-RAY DIFFRACTIONf_plane_restr0.007299
X-RAY DIFFRACTIONf_dihedral_angle_d12.5155208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.460.28241320.22042598X-RAY DIFFRACTION99.96
2.46-29.40.23461490.22012717X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 2.37089744426 Å / Origin y: 16.3912441677 Å / Origin z: -8.59542774899 Å
111213212223313233
T0.169076673818 Å20.0307482950716 Å20.0699108118264 Å2-0.242223545907 Å20.011919200779 Å2--0.27188537879 Å2
L1.32206884759 °20.219275350364 °20.877106774305 °2-4.95899938424 °22.99411394417 °2--3.75817040072 °2
S-0.0641361954456 Å °0.0735022487634 Å °-0.135699818353 Å °-0.132395229014 Å °0.0818597265383 Å °-0.303771465214 Å °-0.018337540771 Å °0.270980306605 Å °-0.0350811196856 Å °
Refinement TLS groupSelection details: chain 'A'

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