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- PDB-9q1h: A7 minibinder in complex with Abp2D -

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Basic information

Entry
Database: PDB / ID: 9q1h
TitleA7 minibinder in complex with Abp2D
Components
  • Abp2D Receptor Binding Domain
  • Minibinder A7
KeywordsPROTEIN BINDING / Inhibitor / Complex / de novo protein / adhesin
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus
Similarity search - Function
: / MrkD-like receptor binding domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily
Similarity search - Domain/homology
P pilus assembly protein, pilin FimA
Similarity search - Component
Biological speciessynthetic construct (others)
Acinetobacter baumannii ACICU (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsLopatto, E.D.B. / Tamadonfar, K.O. / Hultgren, S.J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI029549 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R37AI048689 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI157797 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124169 United States
CitationJournal: Biorxiv / Year: 2025
Title: De Novo Design of Miniprotein Inhibitors of Bacterial Adhesins.
Authors: Chazin-Gray, A.M. / Thompson, T.R. / Lopatto, E.D.B. / Magala, P. / Erickson, P.W. / Hunt, A.C. / Manchenko, A. / Aprikian, P. / Tchesnokova, V. / Basova, I. / Sanick, D.A. / Tamadonfar, K.O. ...Authors: Chazin-Gray, A.M. / Thompson, T.R. / Lopatto, E.D.B. / Magala, P. / Erickson, P.W. / Hunt, A.C. / Manchenko, A. / Aprikian, P. / Tchesnokova, V. / Basova, I. / Sanick, D.A. / Tamadonfar, K.O. / Timm, M.R. / Pinkner, J.S. / Dodson, K.W. / Kang, A. / Joyce, E. / Bera, A.K. / Schmitz, A.J. / Ellebedy, A.H. / Hvorecny, K.L. / Cartwright, M.J. / Vernet, A. / Bardales, S. / White, D. / Klevit, R.E. / Sokurenko, E.V. / Hultgren, S.J. / Baker, D.
History
DepositionAug 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Minibinder A7
B: Abp2D Receptor Binding Domain


Theoretical massNumber of molelcules
Total (without water)26,1372
Polymers26,1372
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-9 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.806, 52.464, 152.121
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 Minibinder A7


Mass: 7255.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein Abp2D Receptor Binding Domain / Abp2D Receptor Binding Domain


Mass: 18882.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ACICU (bacteria)
Gene: ACICU_01810 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U3Y091
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 1.97 Å3/Da / Density % sol: 37.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium acetate pH 4.6, 0.15 M Ammonium acetate, and 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.35→49.6 Å / Num. obs: 46366 / % possible obs: 99.43 % / Redundancy: 2 % / Biso Wilson estimate: 13.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02098 / Net I/σ(I): 17.87
Reflection shellResolution: 1.35→1.398 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.02 / Num. unique obs: 4424 / CC1/2: 0.759 / % possible all: 97.34

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→49.6 Å / SU ML: 0.1262 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9597
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1971 2211 4.77 %
Rwork0.1648 44152 -
obs-46363 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.03 Å2
Refinement stepCycle: LAST / Resolution: 1.35→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 0 80 1823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941792
X-RAY DIFFRACTIONf_angle_d0.96252446
X-RAY DIFFRACTIONf_chiral_restr0.0784286
X-RAY DIFFRACTIONf_plane_restr0.0101312
X-RAY DIFFRACTIONf_dihedral_angle_d5.8064258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.24451140.19642619X-RAY DIFFRACTION96.23
1.38-1.410.25771360.1762702X-RAY DIFFRACTION99.23
1.41-1.450.19421330.15522716X-RAY DIFFRACTION99.3
1.45-1.490.21061300.15422714X-RAY DIFFRACTION99.93
1.49-1.530.20941230.15172775X-RAY DIFFRACTION99.76
1.53-1.580.24261440.14472713X-RAY DIFFRACTION99.93
1.58-1.640.21091440.13242749X-RAY DIFFRACTION99.9
1.64-1.70.19741540.13182720X-RAY DIFFRACTION99.93
1.7-1.780.17721460.14122729X-RAY DIFFRACTION99.83
1.78-1.870.19471320.15312753X-RAY DIFFRACTION98.7
1.87-1.990.1831330.15952783X-RAY DIFFRACTION99.93
1.99-2.140.18191370.16282764X-RAY DIFFRACTION99.83
2.14-2.360.22041470.16842786X-RAY DIFFRACTION99.93
2.36-2.70.22391450.18412787X-RAY DIFFRACTION100
2.7-3.40.19641350.19082827X-RAY DIFFRACTION98.57
3.4-49.60.17181580.15763015X-RAY DIFFRACTION99.78

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