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- PDB-8eja: Computational design of potent and selective inhibitors of Bak and Bax -

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Basic information

Entry
Database: PDB / ID: 8eja
TitleComputational design of potent and selective inhibitors of Bak and Bax
ComponentsaBAK
KeywordsDE NOVO PROTEIN / Computational design / selective inhibitors / Bak / Bax
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsBera, A.K. / Berger, S.A. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Sci Adv / Year: 2025
Title: Computational design of potent and selective binders of BAK and BAX.
Authors: Berger, S. / Lee, E.F. / Harris, T.J. / Tran, S. / Bera, A.K. / Arguinchona, L. / Kang, A. / Sankaran, B. / Kasapgil, S. / Miller, M.S. / Smyth, S. / Lutfi, M. / Uren, R.T. / Kluck, R.M. / ...Authors: Berger, S. / Lee, E.F. / Harris, T.J. / Tran, S. / Bera, A.K. / Arguinchona, L. / Kang, A. / Sankaran, B. / Kasapgil, S. / Miller, M.S. / Smyth, S. / Lutfi, M. / Uren, R.T. / Kluck, R.M. / Colman, P.M. / Fairlie, W.D. / Czabotar, P.E. / Baker, D. / Birkinshaw, R.W.
History
DepositionSep 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: aBAK
A: aBAK


Theoretical massNumber of molelcules
Total (without water)27,6172
Polymers27,6172
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.829, 53.829, 206.038
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

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Components

#1: Protein aBAK


Mass: 13808.640 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Sodium HEPES pH 7.5, 2% (v/v) PEG 400 and 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97901 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2.81→47.71 Å / Num. obs: 8020 / % possible obs: 99.84 % / Redundancy: 8.9 % / Biso Wilson estimate: 65.92 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.051 / Rrim(I) all: 0.1 / Net I/σ(I): 13.4
Reflection shellResolution: 2.81→2.91 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 767 / CC1/2: 0.907 / Rpim(I) all: 0.411 / % possible all: 99.74

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Processing

Software
NameVersionClassification
PHENIX1.18rc2_3793refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Designed model

Resolution: 2.81→47.71 Å / SU ML: 0.3789 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.9121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3084 776 9.69 %
Rwork0.2587 7232 -
obs0.2637 8008 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.6 Å2
Refinement stepCycle: LAST / Resolution: 2.81→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 0 13 1875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231883
X-RAY DIFFRACTIONf_angle_d0.45052508
X-RAY DIFFRACTIONf_chiral_restr0.032273
X-RAY DIFFRACTIONf_plane_restr0.0016333
X-RAY DIFFRACTIONf_dihedral_angle_d14.2377776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.990.34551110.33011185X-RAY DIFFRACTION99.77
2.99-3.220.37021250.30491150X-RAY DIFFRACTION99.84
3.22-3.540.33641340.28331177X-RAY DIFFRACTION99.85
3.54-4.050.34981260.25551184X-RAY DIFFRACTION99.77
4.05-5.10.28261330.23231217X-RAY DIFFRACTION99.93
5.11-47.710.27491470.24621319X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 26.4841165244 Å / Origin y: -0.244819766106 Å / Origin z: 12.6452980282 Å
111213212223313233
T0.496151068809 Å2-0.0541611877787 Å20.0519432651599 Å2-0.570351407325 Å20.015627553396 Å2--0.337601233782 Å2
L0.350055113634 °2-0.417271720354 °20.411793784149 °2-2.87948007325 °2-0.559418436887 °2--0.473506917303 °2
S0.14430299298 Å °-0.0791701816658 Å °0.00998566667555 Å °-0.0901136146398 Å °-0.0621177671466 Å °-0.117369648508 Å °0.0794460217101 Å °0.140349644752 Å °-0.0817394223004 Å °
Refinement TLS groupSelection details: all

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