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- PDB-2zsu: Crystal structure of spermidine synthase from Pyrococcus horikosh... -

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Basic information

Entry
Database: PDB / ID: 2zsu
TitleCrystal structure of spermidine synthase from Pyrococcus horikoshii OT3, P1 form
Componentsspermidine synthase
KeywordsTRANSFERASE / spermidine synthase / aminopropylagmatine / Polyamine biosynthesis / Spermidine biosynthesis
Function / homology
Function and homology information


spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cytoplasm
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
1-{4-[(3-aminopropyl)amino]butyl}guanidine / Polyamine aminopropyltransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMizutani, H. / Kunishima, N.
CitationJournal: To be Published
Title: Crystal structure of spermidine synthase from Pyrococcus horikoshii OT3
Authors: Mizutani, H. / Kunishima, N.
History
DepositionSep 17, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
E: spermidine synthase
F: spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,6279
Polymers192,0656
Non-polymers5623
Water16,754930
1
A: spermidine synthase
B: spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2093
Polymers64,0222
Non-polymers1871
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-10 kcal/mol
Surface area20640 Å2
MethodPISA
2
C: spermidine synthase
D: spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2093
Polymers64,0222
Non-polymers1871
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-8 kcal/mol
Surface area20390 Å2
MethodPISA
3
E: spermidine synthase
F: spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2093
Polymers64,0222
Non-polymers1871
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-10 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.617, 81.842, 96.653
Angle α, β, γ (deg.)99.81, 103.13, 107.85
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
spermidine synthase / / Putrescine aminopropyltransferase / PAPT / SPDSY


Mass: 32010.826 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O57950, spermidine synthase
#2: Chemical ChemComp-AG3 / 1-{4-[(3-aminopropyl)amino]butyl}guanidine / N1-aminopropylagmatine


Mass: 187.286 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H21N5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 930 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.3
Details: 0.2M NH4Cl, 20% w/v PEG 3350, pH 6.3, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jan 17, 2006
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 90319 / Num. obs: 90319 / % possible obs: 95.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.063 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.77 / Num. unique all: 8740 / Rsym value: 0.308 / % possible all: 92.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2E5W

2e5w


Resolution: 2.2→27.92 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1576866.53 / 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
Rfree0.248 4549 5 %RANDOM
Rwork0.207 ---
all0.209 90320 --
obs0.207 90320 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.1681 Å2 / ksol: 0.321984 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.63 Å2-6.29 Å21.86 Å2
2---1.71 Å20.53 Å2
3----4.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.2→27.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13341 0 39 930 14310
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 764 5.2 %
Rwork0.335 13925 -
obs--93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ag3.paramag3.top

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