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- PDB-36ly: Crystal Structure of mini-binder MB07 -

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Basic information

Entry
Database: PDB / ID: 36ly
TitleCrystal Structure of mini-binder MB07
ComponentsMB07
KeywordsAPOPTOSIS / De novo design / deep learning / minibinder / Bacteroides fragilis toxin / receptor / pathology
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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: MB07
B: MB07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,07110
Polymers19,3022
Non-polymers7698
Water543
1
A: MB07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2287
Polymers9,6511
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MB07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8433
Polymers9,6511
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.042, 34.711, 37.038
Angle α, β, γ (deg.)81.614, 70.986, 72.002
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein MB07


Mass: 9651.196 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M Lithium sulfate, 0.1 M Sodium acetate pH 4.5, and 50 % w/v PEG 400

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91992 Å / Relative weight: 1
ReflectionResolution: 2.55→32.97 Å / Num. obs: 4566 / % possible obs: 94.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 39.96 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.085 / Net I/σ(I): 4.1
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 581 / CC1/2: 0.492 / Rpim(I) all: 0.498 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→32.97 Å / SU ML: 0.3775 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.283 456 10 %
Rwork0.2225 4103 -
obs0.2288 4559 94.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.42 Å2
Refinement stepCycle: LAST / Resolution: 2.55→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 40 3 1293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331290
X-RAY DIFFRACTIONf_angle_d0.51461728
X-RAY DIFFRACTIONf_chiral_restr0.0349196
X-RAY DIFFRACTIONf_plane_restr0.0057214
X-RAY DIFFRACTIONf_dihedral_angle_d19.1259534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.920.3441480.25731371X-RAY DIFFRACTION94.11
2.92-3.660.27991550.23841352X-RAY DIFFRACTION95.08
3.7-32.970.26391530.20271380X-RAY DIFFRACTION96.96

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