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- PDB-1jq3: Crystal Structure of Spermidine Synthase in Complex with Transiti... -

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Basic information

Entry
Database: PDB / ID: 1jq3
TitleCrystal Structure of Spermidine Synthase in Complex with Transition State Analogue AdoDATO
ComponentsSpermidine synthase
KeywordsTRANSFERASE / aminopropyltransferase / homo-tetramer / thermophyle / transition-state analogue / beta-barrel / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


sym-norspermidine synthase activity / cadaverine aminopropyltransferase activity / agmatine aminopropyltransferase activity / thermospermine synthase activity / spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cytosol
Similarity search - Function
Spermidine synthase, tetramerisation domain / 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 ...Spermidine synthase, tetramerisation domain / 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 / Spermidine Synthase; Chain: A, domain 2 / Vaccinia Virus protein VP39 / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-1,8-DIAMINO-3-THIOOCTANE / Polyamine aminopropyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKorolev, S. / Ikeguchi, Y. / Skarina, T. / Beasley, S. / Edwards, A. / Joachimiak, A. / Pegg, A.E. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor.
Authors: Korolev, S. / Ikeguchi, Y. / Skarina, T. / Beasley, S. / Arrowsmith, C. / Edwards, A. / Joachimiak, A. / Pegg, A.E. / Savchenko, A.
History
DepositionAug 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spermidine synthase
B: Spermidine synthase
C: Spermidine synthase
D: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,0077
Polymers136,7364
Non-polymers1,2713
Water13,385743
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16630 Å2
ΔGint-93 kcal/mol
Surface area39730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.519, 198.020, 51.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Spermidine synthase / putrescine aminopropyltransferase / SPDSY


Mass: 34184.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZC2, spermidine synthase
#2: Chemical ChemComp-AAT / S-ADENOSYL-1,8-DIAMINO-3-THIOOCTANE


Mass: 423.533 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H29N7O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 4.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 %(w/v)PEG40001reservoir
250 mMsodium acetate1reservoirpH4.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å
DetectorType: SBC-1 / Detector: CCD / Date: May 24, 2001
RadiationMonochromator: Double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 138175 / Num. obs: 126154 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.076
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2 / % possible all: 72.5
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 72.5 % / Rmerge(I) obs: 0.556

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Processing

Software
NameClassification
CNSrefinement
d*TREKdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1INL

1inl


Resolution: 1.8→46.38 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2808531.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 5940 5 %RANDOM
Rwork0.196 ---
obs0.196 118242 93 %-
all-127142 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.4057 Å2 / ksol: 0.335983 e/Å3
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å20 Å20 Å2
2---1.72 Å20 Å2
3---4.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9484 0 87 743 10314
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.252.5
X-RAY DIFFRACTIONc_mcangle_it2.833
X-RAY DIFFRACTIONc_scbond_it3.493
X-RAY DIFFRACTIONc_scangle_it4.83.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 862 4.9 %
Rwork0.251 16807 -
obs-16807 84.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ADO_PAR_10.TXTADO_TOP_7.TXT
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / Num. reflection obs: 112302 / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.26
X-RAY DIFFRACTIONc_mcbond_it2.252.5
X-RAY DIFFRACTIONc_scbond_it3.493
X-RAY DIFFRACTIONc_mcangle_it2.833
X-RAY DIFFRACTIONc_scangle_it4.83.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.29 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.251

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