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- PDB-1inl: Crystal Structure of Spermidine Synthase from Thermotoga Maritima -

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Basic information

Entry
Database: PDB / ID: 1inl
TitleCrystal Structure of Spermidine Synthase from Thermotoga Maritima
ComponentsSpermidine synthase
KeywordsTRANSFERASE / beta-barrel / Rossmann fold / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


sym-norspermidine synthase activity / agmatine aminopropyltransferase activity / cadaverine 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
Polyamine aminopropyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsKorolev, S. / Skarina, T. / Ikeguchi, Y. / Pegg, A.E. / Joachimiak, A. / Edwards, A. / 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
DepositionMay 14, 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 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)136,7364
Polymers136,7364
Non-polymers00
Water15,619867
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13770 Å2
ΔGint-89 kcal/mol
Surface area40770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.436, 197.812, 51.627
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


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 867 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, 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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97925, 0.97938, 0.99187
SYNCHROTRONAPS 19-ID20.97941
Detector
TypeIDDetectorDateDetails
SBC-21CCDMar 28, 2001Double crystal monochromator Si-111
SBC-22CCDMar 7, 2001Double crystal monochromator Si-111
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromator Si-111MADMx-ray1
2Double crystal monochromator Si-111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.979381
30.991871
40.979411
ReflectionResolution: 1.5→50 Å / Num. all: 217343 / Num. obs: 207448 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 23
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4 / % possible all: 81.4
Reflection
*PLUS
% possible obs: 95.2 % / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 81.4 % / Rmerge(I) obs: 0.242

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Processing

Software
NameVersionClassification
d*TREKdata scaling
HKL-2000data reduction
SnBphasing
SOLVEphasing
DMmodel building
CNS0.9refinement
d*TREKdata reduction
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→48.1 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2830560.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 10174 4.9 %RANDOM
Rwork0.199 ---
all0.199 207247 --
obs0.199 207247 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.51 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20 Å2
2---1.34 Å20 Å2
3---2.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.5→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9367 0 0 867 10234
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d1.07
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.245 1512 5 %
Rwork0.223 28847 -
obs--84.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.07
LS refinement shell
*PLUS
Rfactor Rfree: 0.245 / % reflection Rfree: 5 % / Rfactor Rwork: 0.223

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