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- PDB-9q1v: Crystal Structure of de novo design FimH minibinder F7 complex -

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Basic information

Entry
Database: PDB / ID: 9q1v
TitleCrystal Structure of de novo design FimH minibinder F7 complex
Components
  • FimH minibinder F7
  • Type 1 fimbrin D-mannose specific adhesin
KeywordsDE NOVO PROTEIN / de novo design / multidrug-resistant / bacterial infections / Bacterial Adhesins / Miniprotein Inhibitors
Function / homology
Function and homology information


pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / cell adhesion
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily
Similarity search - Domain/homology
Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciessynthetic construct (others)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBera, A.K. / Kang, A. / Thomson, T. / Chazin-Gray, A. / Baker, D.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Defense Advanced Research Projects Agency (DARPA)HR0011-21-2- 0012 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 14, 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

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Assembly

Deposited unit
A: FimH minibinder F7
B: Type 1 fimbrin D-mannose specific adhesin
C: FimH minibinder F7
D: Type 1 fimbrin D-mannose specific adhesin


Theoretical massNumber of molelcules
Total (without water)49,0114
Polymers49,0114
Non-polymers00
Water4,252236
1
A: FimH minibinder F7
B: Type 1 fimbrin D-mannose specific adhesin


Theoretical massNumber of molelcules
Total (without water)24,5052
Polymers24,5052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-7 kcal/mol
Surface area10300 Å2
MethodPISA
2
C: FimH minibinder F7
D: Type 1 fimbrin D-mannose specific adhesin


Theoretical massNumber of molelcules
Total (without water)24,5052
Polymers24,5052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-8 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.967, 52.387, 72.865
Angle α, β, γ (deg.)90.000, 101.795, 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 FimH minibinder F7


Mass: 6795.729 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: Protein Type 1 fimbrin D-mannose specific adhesin / Protein FimH


Mass: 17709.635 Da / Num. of mol.: 2 / Mutation: L34K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimH, b4320, JW4283 / Production host: Escherichia coli (E. coli) / References: UniProt: P08191
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 1.95 Å3/Da / Density % sol: 36.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M sodium malonate, pH 7.0, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 25, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.75→42.22 Å / Num. obs: 34397 / % possible obs: 90.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.58 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.072 / Net I/σ(I): 5.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2003 / CC1/2: 0.753 / Rpim(I) all: 0.397 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→42.22 Å / SU ML: 0.2398 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.8031
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.263 1415 4.12 %
Rwork0.233 32911 -
obs0.2343 34326 90 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.06 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 0 236 3684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423529
X-RAY DIFFRACTIONf_angle_d0.65024829
X-RAY DIFFRACTIONf_chiral_restr0.0492558
X-RAY DIFFRACTIONf_plane_restr0.0054632
X-RAY DIFFRACTIONf_dihedral_angle_d15.09871213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.39571500.37093482X-RAY DIFFRACTION95.91
1.81-1.890.34541340.33693128X-RAY DIFFRACTION86.5
1.89-1.970.34941140.30182652X-RAY DIFFRACTION72.43
1.97-2.070.30381290.26342985X-RAY DIFFRACTION82.47
2.07-2.20.25821510.24653521X-RAY DIFFRACTION96.28
2.2-2.370.28711390.24273219X-RAY DIFFRACTION88.98
2.38-2.610.27491530.23663583X-RAY DIFFRACTION97.7
2.61-2.990.27951440.24043358X-RAY DIFFRACTION91.53
2.99-3.770.25531440.20533347X-RAY DIFFRACTION91.41
3.77-42.220.18821570.17383636X-RAY DIFFRACTION96.64
Refinement TLS params.Method: refined / Origin x: 20.147186564 Å / Origin y: 14.2262954809 Å / Origin z: 17.7809713159 Å
111213212223313233
T0.0592514348082 Å20.00243895800278 Å20.00508799019756 Å2-0.0866912108507 Å2-0.0104205769878 Å2--0.0648517591684 Å2
L0.105327207065 °2-0.0274150074336 °20.116406131584 °2-0.0190775968246 °2-0.0389848469695 °2--0.116238879607 °2
S-0.0137638029415 Å °0.070507946832 Å °0.0190311645412 Å °-0.00158760338882 Å °-0.0110721395729 Å °0.00403870408308 Å °-0.00325157185188 Å °0.0357642447946 Å °-0.0903950638041 Å °
Refinement TLS groupSelection details: all

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