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- PDB-3wr7: Crystal Structure of Spermidine Acetyltransferase from Escherichi... -

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Basic information

Entry
Database: PDB / ID: 3wr7
TitleCrystal Structure of Spermidine Acetyltransferase from Escherichia coli
ComponentsSpermidine N1-acetyltransferase
KeywordsTRANSFERASE / alpha and beta
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / SPERMIDINE / Spermidine N1-acetyltransferase / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSugiyama, S. / Ishikawa, S. / Tomitori, S. / Niiyama, M. / Hirose, M. / Miyazaki, Y. / Higashi, K. / Adachi, H. / Takano, K. / Murakami, S. ...Sugiyama, S. / Ishikawa, S. / Tomitori, S. / Niiyama, M. / Hirose, M. / Miyazaki, Y. / Higashi, K. / Adachi, H. / Takano, K. / Murakami, S. / Inoue, T. / Mori, Y. / Kashiwagi, K. / Igarashi, K. / Matsumura, H.
CitationJournal: Int.J.Biochem.Cell Biol. / Year: 2016
Title: Molecular mechanism underlying promiscuous polyamine recognition by spermidine acetyltransferase
Authors: Sugiyama, S. / Ishikawa, S. / Tomitori, H. / Niiyama, M. / Hirose, M. / Miyazaki, Y. / Higashi, K. / Murata, M. / Adachi, H. / Takano, K. / Murakami, S. / Inoue, T. / Mori, Y. / Kashiwagi, K. ...Authors: Sugiyama, S. / Ishikawa, S. / Tomitori, H. / Niiyama, M. / Hirose, M. / Miyazaki, Y. / Higashi, K. / Murata, M. / Adachi, H. / Takano, K. / Murakami, S. / Inoue, T. / Mori, Y. / Kashiwagi, K. / Igarashi, K. / Matsumura, H.
History
DepositionFeb 20, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Spermidine N1-acetyltransferase
C: Spermidine N1-acetyltransferase
B: Spermidine N1-acetyltransferase
D: Spermidine N1-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,83612
Polymers81,1854
Non-polymers3,6518
Water3,063170
1
A: Spermidine N1-acetyltransferase
C: Spermidine N1-acetyltransferase
B: Spermidine N1-acetyltransferase
D: Spermidine N1-acetyltransferase
hetero molecules

A: Spermidine N1-acetyltransferase
C: Spermidine N1-acetyltransferase
B: Spermidine N1-acetyltransferase
D: Spermidine N1-acetyltransferase
hetero molecules

A: Spermidine N1-acetyltransferase
C: Spermidine N1-acetyltransferase
B: Spermidine N1-acetyltransferase
D: Spermidine N1-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,50736
Polymers243,55412
Non-polymers10,95324
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area52490 Å2
ΔGint15 kcal/mol
Surface area81020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.688, 148.688, 148.688
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

#1: Protein
Spermidine N1-acetyltransferase


Mass: 20296.139 Da / Num. of mol.: 4 / Fragment: UNP residues 5-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: LY180 / Production host: Escherichia coli (E. coli) / References: UniProt: T2FY33, UniProt: A0A0M3KKU5*PLUS
#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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50mM sodium cacodylate pH 6.5, 9%(w/v) PEG 8000, 0.1M calcium acetate., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2009
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 38070 / % possible obs: 99.9 % / Rmerge(I) obs: 0.094

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.02 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 10.175 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27595 1917 5 %RANDOM
Rwork0.21253 ---
obs0.21566 36114 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.414 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5724 0 232 170 6126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0216108
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.9818237
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8085678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84723.412337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.967151059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4371549
X-RAY DIFFRACTIONr_chiral_restr0.1760.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024629
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9981.53382
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91225435
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.65132726
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1374.52802
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 141 -
Rwork0.288 2681 -
obs--99.82 %

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