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- PDB-3c6k: Crystal structure of human spermine synthase in complex with sper... -

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Basic information

Entry
Database: PDB / ID: 3c6k
TitleCrystal structure of human spermine synthase in complex with spermidine and 5-methylthioadenosine
ComponentsSpermine synthase
KeywordsTRANSFERASE / SPERMIDINE AMINOPROPYLTRANSFERASE / SPMSY / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Phosphoprotein
Function / homology
Function and homology information


spermine synthase / spermine synthase activity / spermine biosynthetic process / Metabolism of polyamines / polyamine metabolic process / methionine metabolic process / extracellular exosome / cytosol
Similarity search - Function
Spermine synthase, animal / Spermine synthase, N-terminal / S-adenosylmethionine decarboxylase N -terminal / Sirohaem synthase, central domain / Spermidine synthase, tetramerisation domain / Polyamine biosynthesis domain, conserved site / Polyamine biosynthesis (PABS) domain signature. / Polyamine biosynthesis domain / Spermidine synthase, tetramerisation domain / Spermidine synthase, tetramerisation domain superfamily ...Spermine synthase, animal / Spermine synthase, N-terminal / S-adenosylmethionine decarboxylase N -terminal / Sirohaem synthase, central domain / Spermidine synthase, tetramerisation domain / Polyamine biosynthesis domain, conserved site / Polyamine biosynthesis (PABS) domain signature. / 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 / Double Stranded RNA Binding Domain / Vaccinia Virus protein VP39 / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / SPERMIDINE / Spermine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMin, J. / Wu, H. / Zeng, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Pegg, A.E. ...Min, J. / Wu, H. / Zeng, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Pegg, A.E. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism.
Authors: Wu, H. / Min, J. / Zeng, H. / McCloskey, D.E. / Ikeguchi, Y. / Loppnau, P. / Michael, A.J. / Pegg, A.E. / Plotnikov, A.N.
History
DepositionFeb 4, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 19, 2008ID: 2QFM
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Spermine synthase
B: Spermine synthase
C: Spermine synthase
D: Spermine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,78212
Polymers172,0114
Non-polymers1,7708
Water20,9691164
1
A: Spermine synthase
B: Spermine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8916
Polymers86,0062
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
MethodPISA
2
C: Spermine synthase
D: Spermine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8916
Polymers86,0062
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.385, 74.032, 143.226
Angle α, β, γ (deg.)94.23, 92.88, 107.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Spermine synthase / Spermidine aminopropyltransferase / SPMSY


Mass: 43002.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMS / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RIL / References: UniProt: P52788, spermine synthase
#2: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H19N3
#3: Chemical
ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N5O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1164 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 20000, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54178 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 12, 2006 / Details: var
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 115647 / Num. obs: 115647 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2O06

2o06


Resolution: 1.95→40.56 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.895 / SU B: 3.886 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25744 5758 5 %RANDOM
Rwork0.19776 ---
all0.2007 109886 --
obs0.2007 109886 93.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.798 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0.55 Å2-0.13 Å2
2---1.33 Å2-0.14 Å2
3---1.81 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10956 0 120 1164 12240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02211287
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9915215
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96451351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92524.871505
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.512152065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.331554
X-RAY DIFFRACTIONr_chiral_restr0.1170.21700
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028270
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.24970
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.27474
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.21095
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.297
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2650.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.091.57042
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.699210941
X-RAY DIFFRACTIONr_scbond_it2.58734985
X-RAY DIFFRACTIONr_scangle_it3.8194.54274
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 288 -
Rwork0.219 5228 -
obs--60.54 %

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