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- PDB-36mb: Crystal Structure of mini-binder MB07-ds -

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Basic information

Entry
Database: PDB / ID: 36mb
TitleCrystal Structure of mini-binder MB07-ds
ComponentsMB07-ds
KeywordsAPOPTOSIS / De novo design / deep learning / minibinder / Bacteroides fragilis toxin / receptor / pathology
Function / homologyPROLINE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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-ds
B: MB07-ds
C: MB07-ds
D: MB07-ds
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9367
Polymers38,6294
Non-polymers3073
Water1,33374
1
A: MB07-ds
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8683
Polymers9,6571
Non-polymers2112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MB07-ds


Theoretical massNumber of molelcules
Total (without water)9,6571
Polymers9,6571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MB07-ds


Theoretical massNumber of molelcules
Total (without water)9,6571
Polymers9,6571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MB07-ds
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7532
Polymers9,6571
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.306, 51.306, 56.008
Angle α, β, γ (deg.)90.000, 90.949, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
MB07-ds


Mass: 9657.290 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1 M Citric acid pH 3.5, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97905 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 10, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 2→56 Å / Num. obs: 26405 / % possible obs: 99.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 31.45 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.097 / Net I/σ(I): 5.23
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.361 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 1891 / CC1/2: 0.566 / Rpim(I) all: 0.585 / % possible all: 99.41

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→56 Å / SU ML: 0.2415 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.9316
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2663 2010 9.48 %
Rwork0.2267 19197 -
obs0.2305 21207 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.06 Å2
Refinement stepCycle: LAST / Resolution: 2→56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2579 0 18 74 2671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312629
X-RAY DIFFRACTIONf_angle_d0.53783516
X-RAY DIFFRACTIONf_chiral_restr0.0367403
X-RAY DIFFRACTIONf_plane_restr0.0035445
X-RAY DIFFRACTIONf_dihedral_angle_d23.01251105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.34771550.29191367X-RAY DIFFRACTION99.41
2.05-2.110.31391300.27021340X-RAY DIFFRACTION98.92
2.11-2.170.29121410.26291372X-RAY DIFFRACTION98.82
2.17-2.240.34191440.25311366X-RAY DIFFRACTION99.47
2.24-2.320.31931450.25491336X-RAY DIFFRACTION98.41
2.32-2.410.30371410.2381354X-RAY DIFFRACTION98.16
2.41-2.520.30761470.24391380X-RAY DIFFRACTION99.67
2.52-2.650.2721400.25121364X-RAY DIFFRACTION99.73
2.65-2.820.28581430.23191384X-RAY DIFFRACTION100
2.82-3.040.31311440.24251375X-RAY DIFFRACTION99.02
3.04-3.340.29731450.24061363X-RAY DIFFRACTION99.02
3.34-3.830.23871400.20071370X-RAY DIFFRACTION98.56
3.83-4.820.22731510.18171395X-RAY DIFFRACTION99.74
4.82-560.2191440.23061431X-RAY DIFFRACTION98.56
Refinement TLS params.Method: refined / Origin x: 12.2901797965 Å / Origin y: -13.8152137694 Å / Origin z: 15.7627740217 Å
111213212223313233
T0.257922518998 Å20.00856294859431 Å2-0.0567832545737 Å2-0.2327774588 Å2-0.00679559912885 Å2--0.246913407665 Å2
L0.275214340834 °20.0378335821943 °2-0.247382585614 °2-0.303355415305 °2-0.0424649879383 °2--0.262863935171 °2
S-0.0050676613805 Å °-0.0611717172209 Å °-0.0075440550757 Å °0.0412613157852 Å °0.0209381086889 Å °-0.0664971036399 Å °-0.0159738550169 Å °0.0899145143433 Å °-0.0176969011533 Å °
Refinement TLS groupSelection details: all

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