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

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Basic information

Entry
Database: PDB / ID: 9lns
TitleCrystal structure of de novo designed amantadine induced homotrimer dAIT17
ComponentsdAIT17
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: 1.5 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: dAIT17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7663
Polymers7,4641
Non-polymers3022
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.159, 79.159, 79.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-101-

308

21A-101-

308

31A-102-

308

41A-102-

308

51A-274-

HOH

61A-292-

HOH

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Components

#1: Protein dAIT17


Mass: 7463.866 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-308 / (3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine / Amantadine


Mass: 151.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 22% w/v Polyethylene glycol 1,000

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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 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→27.99 Å / Num. obs: 14121 / % possible obs: 99.67 % / Redundancy: 3.7 % / CC1/2: 1 / Net I/σ(I): 22.56
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 1374 / CC1/2: 0.665

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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: 1.5→27.99 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 1411 10.02 %
Rwork0.1978 --
obs0.2012 14085 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms543 0 0 111 654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013547
X-RAY DIFFRACTIONf_angle_d1.339733
X-RAY DIFFRACTIONf_dihedral_angle_d4.22865
X-RAY DIFFRACTIONf_chiral_restr0.06293
X-RAY DIFFRACTIONf_plane_restr0.00884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.25541380.22381236X-RAY DIFFRACTION100
1.55-1.620.30231360.22231237X-RAY DIFFRACTION100
1.62-1.690.26451380.19451237X-RAY DIFFRACTION100
1.69-1.780.32091370.21261238X-RAY DIFFRACTION100
1.78-1.890.27571400.22111254X-RAY DIFFRACTION100
1.89-2.040.23321400.21661260X-RAY DIFFRACTION100
2.04-2.240.27971400.17871260X-RAY DIFFRACTION99
2.24-2.560.24251410.1941257X-RAY DIFFRACTION99
2.57-3.230.18211440.19281293X-RAY DIFFRACTION99
3.23-27.990.21411570.19321402X-RAY DIFFRACTION100

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