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- PDB-8iyi: Spermidine synthase from Kluyveromyces lactis -

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Basic information

Entry
Database: PDB / ID: 8iyi
TitleSpermidine synthase from Kluyveromyces lactis
ComponentsKLLA0B09372p
KeywordsTRANSFERASE / Spermidine / Synthase / aminopropyltransferase
Function / homology
Function and homology information


polyamine biosynthetic process / transferase activity
Similarity search - Function
Spermidine/spermine synthase, eukaryotes / Polyamine biosynthesis domain, conserved site / Polyamine biosynthesis (PABS) domain signature. / Spermidine/spermine synthases / Polyamine biosynthesis domain / Spermidine synthase, tetramerisation domain / Spermidine synthase, tetramerisation domain superfamily / Spermidine synthase tetramerisation domain / Polyamine biosynthesis (PABS) domain profile. / Spermine/spermidine synthase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, S. / Chang, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2022R1F1A1073775 Korea, Republic Of
CitationJournal: Molecules / Year: 2023
Title: Structural Analysis of Spermidine Synthase from Kluyveromyces lactis.
Authors: Kim, S. / Chang, J.H.
History
DepositionApr 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KLLA0B09372p
B: KLLA0B09372p


Theoretical massNumber of molelcules
Total (without water)66,5862
Polymers66,5862
Non-polymers00
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-17 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.252, 98.180, 102.134
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 KLLA0B09372p / Spermidine Synthase


Mass: 33292.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Gene: KLLA0_B09372g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CVU4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 9.2% v/v TacsimateTM pH 5.0, 16.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 52396 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 19.8 Å2 / CC1/2: 0.996 / Net I/σ(I): 33
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 5161 / CC1/2: 0.965

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.98 Å / SU ML: 0.1535 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.471 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1987 1979 3.84 %
Rwork0.1681 49584 -
obs0.1692 51563 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4631 0 0 555 5186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00684753
X-RAY DIFFRACTIONf_angle_d0.81836454
X-RAY DIFFRACTIONf_chiral_restr0.0575721
X-RAY DIFFRACTIONf_plane_restr0.0049820
X-RAY DIFFRACTIONf_dihedral_angle_d2.76763406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.22471310.17983303X-RAY DIFFRACTION93.57
1.95-20.19291310.17273436X-RAY DIFFRACTION96.28
2-2.060.21631370.17563431X-RAY DIFFRACTION97.25
2.06-2.130.261440.17223498X-RAY DIFFRACTION97.93
2.13-2.20.20411380.16653476X-RAY DIFFRACTION98.21
2.2-2.290.21171360.16753526X-RAY DIFFRACTION98.71
2.29-2.390.20711460.16313527X-RAY DIFFRACTION98.9
2.39-2.520.20151470.17613545X-RAY DIFFRACTION99.33
2.52-2.680.20961400.17563558X-RAY DIFFRACTION99.3
2.68-2.890.21271390.17463577X-RAY DIFFRACTION99.46
2.89-3.180.20751470.1643589X-RAY DIFFRACTION99.76
3.18-3.640.16691460.15843653X-RAY DIFFRACTION99.95
3.64-4.580.16251450.14943641X-RAY DIFFRACTION99.95
4.58-47.980.21731520.18573824X-RAY DIFFRACTION99.8

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