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- PDB-22it: Crystal structure of LbSCT1 in complex with Spermidine -

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Basic information

Entry
Database: PDB / ID: 22it
TitleCrystal structure of LbSCT1 in complex with Spermidine
ComponentsCaffeoyltransferase
KeywordsTRANSFERASE / Lycibarbarspermidines / Biosynthesis / Caffeoyltransferase
Function / homologySPERMIDINE
Function and homology information
Biological speciesLycium barbarum (goji berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12007993639 Å
AuthorsWang, G.Q. / Hu, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural and catalytic mechanistic insights into caffeoyltransferase underpin lycibarbarspermidine biosynthesis in Lycium barbarum
Authors: Li, S.Y. / Wang, G.Q. / Hu, D.
History
DepositionJan 13, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caffeoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0643
Polymers52,7731
Non-polymers2902
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.340, 64.340, 113.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Caffeoyltransferase


Mass: 52773.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lycium barbarum (goji berry) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Sodium cacodylate pH 5.5, 25% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.12→32.7 Å / Num. obs: 26258 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 37.6073328437 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.6
Reflection shellResolution: 2.12→2.18 Å / Num. unique obs: 1920 / CC1/2: 0.626

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
xia2data reduction
xia2data scaling
PHENIX1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12007993639→32.6640856572 Å / SU ML: 0.249837325376 / Cross valid method: FREE R-VALUE / σ(F): 1.33783093408 / Phase error: 27.2385608105
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.256047699474 1351 5.1525553013 %
Rwork0.218443703758 24869 -
obs0.220365195409 26220 99.9923728167 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.3660456435 Å2
Refinement stepCycle: LAST / Resolution: 2.12007993639→32.6640856572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 20 124 3658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002635049031553615
X-RAY DIFFRACTIONf_angle_d0.5027033142534889
X-RAY DIFFRACTIONf_chiral_restr0.0414595157287542
X-RAY DIFFRACTIONf_plane_restr0.00560329652263634
X-RAY DIFFRACTIONf_dihedral_angle_d3.485312542032202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1201-2.19580.28714814311270.2860303549382442X-RAY DIFFRACTION100
2.1958-2.28370.3280748882111260.2783712194522525X-RAY DIFFRACTION100
2.2837-2.38760.3136984188161160.2716755141332518X-RAY DIFFRACTION100
2.3876-2.51350.260286980921410.2661258592532460X-RAY DIFFRACTION100
2.5135-2.67090.3147422798821520.2642837540942462X-RAY DIFFRACTION100
2.6709-2.8770.3075854599811560.2565073419512447X-RAY DIFFRACTION100
2.877-3.16630.3479293164411330.2502088407912490X-RAY DIFFRACTION100
3.1663-3.6240.2757618418531250.2168938366032504X-RAY DIFFRACTION100
3.624-4.56380.2280915571651450.1854881283442496X-RAY DIFFRACTION100

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