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- PDB-2b2c: Cloning, expression, characterisation and three- dimensional stru... -

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Basic information

Entry
Database: PDB / ID: 2b2c
TitleCloning, expression, characterisation and three- dimensional structure determination of the Caenorhabditis elegans spermidine synthase
Componentsspermidine synthase
KeywordsTRANSFERASE / beta-alpha
Function / homology
Function and homology information


spermidine synthase / spermidine synthase activity / polyamine biosynthetic process / spermidine biosynthetic process
Similarity search - Function
Spermidine/spermine synthase, eukaryotes / 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. ...Spermidine/spermine synthase, eukaryotes / 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
PABS domain-containing protein / :
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDufe, V.T. / Luersen, K. / Eschbach, M.L. / Haider, N. / Karlberg, T. / Walter, R.D. / Al-Karadaghi, S.
CitationJournal: FEBS LETT. / Year: 2005
Title: Cloning, expression, characterisation and three-dimensional structure determination of Caenorhabditis elegans spermidine synthase
Authors: Dufe, V.T. / Luersen, K. / Eschbach, M.L. / Haider, N. / Karlberg, T. / Walter, R.D. / Al-Karadaghi, S.
History
DepositionSep 19, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: spermidine synthase
B: spermidine synthase


Theoretical massNumber of molelcules
Total (without water)70,1422
Polymers70,1422
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-17 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.990, 99.230, 67.850
Angle α, β, γ (deg.)90.00, 107.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 3 - 314 / Label seq-ID: 3 - 314

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological assembly is the two molecules in the assymmetric unit.

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Components

#1: Protein spermidine synthase


Mass: 35070.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: pTrcHisB / Production host: Escherichia coli (E. coli)
References: UniProt: Q9U2F0, UniProt: G5EFG3*PLUS, spermidine synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.8 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 3350, Lithium sulfate, Tris-CL, Dithiothreitol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 75.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.89978 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89978 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 25260 / Num. obs: 25260 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.108
Reflection shellResolution: 2.5→2.65 Å / % possible all: 88.77

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.469 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.425 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25415 1312 5 %RANDOM
Rwork0.219 ---
all0.22 24926 --
obs0.22032 24926 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.039 Å2
Baniso -1Baniso -2Baniso -3
1-8.42 Å20 Å22.35 Å2
2---5.09 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 0 84 4462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224482
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9586060
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6725546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86924.455202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.74215774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0321516
X-RAY DIFFRACTIONr_chiral_restr0.1090.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023360
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.21969
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22973
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0880.27
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.44522811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.96454420
X-RAY DIFFRACTIONr_scbond_it5.10671874
X-RAY DIFFRACTIONr_scangle_it7.392101640
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2183 / Refine-ID: X-RAY DIFFRACTION

RmsTypeWeight
0.07TIGHT POSITIONAL0.05
0.13TIGHT THERMAL0.5
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 93 -
Rwork0.371 1770 -
all-1863 -
obs--100 %

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