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- PDB-9lnt: Crystal structure of de novo designed amantadine induced homotrim... -

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Basic information

Entry
Database: PDB / ID: 9lnt
TitleCrystal structure of de novo designed amantadine induced homotrimer mAIT03
ComponentsmAIT03
KeywordsDE NOVO PROTEIN / Drug induced homotrimer
Function / homology(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsQihan, J. / Longxing, C.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA1303700 China
CitationJournal: Science / Year: 2026
Title: De novo design of small molecule-regulated protein oligomers.
Authors: Jin, Q. / Wang, Y. / Chen, D. / Liao, J. / Cui, Z. / Fan, Y. / Zeng, A. / Xie, M. / Cao, L.
History
DepositionJan 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mAIT03
C: mAIT03
E: mAIT03
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3698
Polymers19,6123
Non-polymers7565
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-14 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.818, 58.000, 40.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-202-

UNX

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Components

#1: Protein mAIT03


Mass: 6537.449 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-UNX / UNKNOWN LIGAND


Mass: 151.249 Da / Num. of mol.: 4 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-308 / (3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine / Amantadine


Mass: 151.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.005 M Cobalt(II) chloride hexahydrate, 0.005 M Nickel(II) chloride hexahydrate, 0.005 M Cadmium chloride hydrate, 0.005 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 181 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.9→29 Å / Num. obs: 15326 / % possible obs: 99.87 % / Redundancy: 3.7 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 27.84
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 1511 / CC1/2: 0.829

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2909 1533 10 %
Rwork0.2475 --
obs-15323 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 15 108 1494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011384
X-RAY DIFFRACTIONf_angle_d1.1251860
X-RAY DIFFRACTIONf_dihedral_angle_d5.344186
X-RAY DIFFRACTIONf_chiral_restr0.061226
X-RAY DIFFRACTIONf_plane_restr0.011246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.33231380.28461241X-RAY DIFFRACTION100
1.96-2.030.29751350.25411224X-RAY DIFFRACTION100
2.03-2.110.31281360.22471218X-RAY DIFFRACTION100
2.11-2.210.25921380.21751234X-RAY DIFFRACTION100
2.21-2.330.26731370.21231236X-RAY DIFFRACTION100
2.33-2.470.24231380.20741237X-RAY DIFFRACTION100
2.47-2.660.28041380.22461246X-RAY DIFFRACTION100
2.66-2.930.29491400.22081258X-RAY DIFFRACTION100
2.93-3.350.25821390.21841256X-RAY DIFFRACTION100
3.35-4.220.25511430.18471285X-RAY DIFFRACTION100
4.22-290.22261510.18431355X-RAY DIFFRACTION100

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