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- PDB-3bj8: Spermine/spermidine N1-acetyltransferase from mouse: Crystal stru... -

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Basic information

Entry
Database: PDB / ID: 3bj8
TitleSpermine/spermidine N1-acetyltransferase from mouse: Crystal structure of a ternary complex reveals solvent-mediated spermine binding
ComponentsDiamine acetyltransferase 1
KeywordsTRANSFERASE / SSAT / CoA / Spermine / Ternary complex / Acyltransferase / Cytoplasm
Function / homology
Function and homology information


Interconversion of polyamines / spermidine acetylation / spermidine binding / putrescine catabolic process / polyamine biosynthetic process / spermine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / N-acetyltransferase activity / regulation of cell population proliferation ...Interconversion of polyamines / spermidine acetylation / spermidine binding / putrescine catabolic process / polyamine biosynthetic process / spermine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / N-acetyltransferase activity / regulation of cell population proliferation / angiogenesis / identical protein binding / cytosol
Similarity search - Function
: / Acetyltransferase (GNAT) family / 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 / SPERMINE / Diamine acetyltransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMontemayor, E.J. / Hoffman, D.W.
CitationJournal: Biochemistry / Year: 2008
Title: The crystal structure of spermidine/spermine N1-acetyltransferase in complex with spermine provides insights into substrate binding and catalysis.
Authors: Montemayor, E.J. / Hoffman, D.W.
History
DepositionDec 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
A: Diamine acetyltransferase 1
B: Diamine acetyltransferase 1
C: Diamine acetyltransferase 1
D: Diamine acetyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4209
Polymers80,1484
Non-polymers3,2725
Water3,837213
1
A: Diamine acetyltransferase 1
B: Diamine acetyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6094
Polymers40,0742
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
MethodPISA
2
C: Diamine acetyltransferase 1
D: Diamine acetyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8115
Polymers40,0742
Non-polymers1,7373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.250, 97.120, 105.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Diamine acetyltransferase 1 / Spermidine/spermine N(1)-acetyltransferase 1 / SSAT / SSAT-1 / Putrescine acetyltransferase / ...Spermidine/spermine N(1)-acetyltransferase 1 / SSAT / SSAT-1 / Putrescine acetyltransferase / Polyamine N-acetyltransferase 1


Mass: 20036.943 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sat1, Sat / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P48026, diamine N-acetyltransferase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→39 Å / Num. all: 35462 / Num. obs: 35462 / Biso Wilson estimate: 23.3 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.98 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1261162.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1744 5 %RANDOM
Rwork0.232 ---
obs0.232 35223 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.2484 Å2 / ksol: 0.340782 e/Å3
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.65 Å20 Å20 Å2
2---4.51 Å20 Å2
3----1.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→33.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5328 0 206 213 5747
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 254 4.4 %
Rwork0.285 5513 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3coa.paramcoa.top
X-RAY DIFFRACTION4spm.paramspm.top

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