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- PDB-36lx: Crystal Structure of mini-binder MB03-ds -

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Basic information

Entry
Database: PDB / ID: 36lx
TitleCrystal Structure of mini-binder MB03-ds
ComponentsMB03-ds
KeywordsAPOPTOSIS / De novo design / deep learning / minibinder / Bacteroides fragilis toxin / receptor / pathology
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBera, A.K. / Adebomi, V. / Srinivas, P. / Kang, A. / Bhardwaj, G.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA)HR0011 21 2 0012 United States
CitationJournal: Biorxiv / Year: 2026
Title: Orally available designed miniproteins inhibit enterotoxigenic Bacteroides fragilis pathology by blocking toxin receptor binding.
Authors: Srinivas, P. / Adebomi, V. / Markiewicz, S.M. / Wang, K. / Chac, D. / Lindenauer, K. / Huber, N. / Tao, Z. / Luong, P. / Rettie, S.A. / Smith, M.W. / Bera, A.K. / Kang, A. / Nguyen, H. / ...Authors: Srinivas, P. / Adebomi, V. / Markiewicz, S.M. / Wang, K. / Chac, D. / Lindenauer, K. / Huber, N. / Tao, Z. / Luong, P. / Rettie, S.A. / Smith, M.W. / Bera, A.K. / Kang, A. / Nguyen, H. / Schneider, M. / Wang, Y. / Peterson, S.B. / Dong, M. / Weil, A.A. / Bhardwaj, G. / Mougous, J.D.
History
DepositionJun 17, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MB03-ds
B: MB03-ds
C: MB03-ds
D: MB03-ds


Theoretical massNumber of molelcules
Total (without water)30,7154
Polymers30,7154
Non-polymers00
Water77543
1
A: MB03-ds


Theoretical massNumber of molelcules
Total (without water)7,6791
Polymers7,6791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MB03-ds


Theoretical massNumber of molelcules
Total (without water)7,6791
Polymers7,6791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MB03-ds


Theoretical massNumber of molelcules
Total (without water)7,6791
Polymers7,6791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MB03-ds


Theoretical massNumber of molelcules
Total (without water)7,6791
Polymers7,6791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.265, 57.412, 93.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
MB03-ds


Mass: 7678.713 Da / Num. of mol.: 4
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.: 43 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 24 %(w/v) PEG 1500 and 20% (w/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.91992 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 2, 2025 / Details: Horizontal secondary source 2 stage focusing
RadiationMonochromator: Horizontal double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91992 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 14230 / % possible obs: 98 % / Redundancy: 8 % / Biso Wilson estimate: 30.8 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.084 / Net I/σ(I): 7.9
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.945 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1036 / CC1/2: 0.719 / Rpim(I) all: 0.414 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40 Å / SU ML: 0.2874 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0603
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2882 1408 10 %
Rwork0.2534 12669 -
obs0.2568 14077 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.91 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 0 43 1905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00281898
X-RAY DIFFRACTIONf_angle_d0.47642535
X-RAY DIFFRACTIONf_chiral_restr0.0309288
X-RAY DIFFRACTIONf_plane_restr0.0022318
X-RAY DIFFRACTIONf_dihedral_angle_d20.6051765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.3561270.31221146X-RAY DIFFRACTION90.16
2.18-2.260.3171340.28061197X-RAY DIFFRACTION93.73
2.26-2.370.29871370.27221246X-RAY DIFFRACTION96.92
2.37-2.490.29071400.26481263X-RAY DIFFRACTION98.04
2.49-2.650.32441400.26751257X-RAY DIFFRACTION99.08
2.65-2.850.30751420.26341283X-RAY DIFFRACTION99.23
2.85-3.140.34921440.27351295X-RAY DIFFRACTION98.97
3.14-3.590.28071440.24911290X-RAY DIFFRACTION98.49
3.59-4.520.26241460.22261303X-RAY DIFFRACTION98.44
4.52-400.25431540.24641389X-RAY DIFFRACTION98.91

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