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- PDB-2b3u: Human Spermine spermidine acetyltransferase K26R mutant -

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Basic information

Entry
Database: PDB / ID: 2b3u
TitleHuman Spermine spermidine acetyltransferase K26R mutant
ComponentsDiamine acetyltransferase 1
KeywordsTRANSFERASE / Acyltransferase / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Interconversion of polyamines / spermidine acetylation / spermidine binding / putrescine catabolic process / polyamine biosynthetic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / N-acetyltransferase activity / regulation of cell population proliferation / angiogenesis ...Interconversion of polyamines / spermidine acetylation / spermidine binding / putrescine catabolic process / polyamine biosynthetic 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
Diamine acetyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsBewley, M.C. / Graziano, V. / Jiang, J.S. / Matz, E. / Studier, F.W. / Pegg, A.P. / Coleman, C.S. / Flanagan, J.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Structures of wild-type and mutant human spermidine/spermine N1-acetyltransferase, a potential therapeutic drug target.
Authors: Bewley, M.C. / Graziano, V. / Jiang, J. / Matz, E. / Studier, F.W. / Pegg, A.E. / Coleman, C.S. / Flanagan, J.M.
History
DepositionSep 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 24, 2015Group: Data collection / Database references
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,0014
Polymers40,8092
Non-polymers1922
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-78 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.3, 74.3, 63.3
Angle α, β, γ (deg.)90, 90, 90
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Diamine acetyltransferase 1 / Spermidine/spermine N1 / - acetyltransferase 1 / SSAT / SSAT-1 / Putrescine acetyltransferase / ...Spermidine/spermine N1 / - acetyltransferase 1 / SSAT / SSAT-1 / Putrescine acetyltransferase / Polyamine N-acetyltransferase 1


Mass: 20404.268 Da / Num. of mol.: 2 / Mutation: K26R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAT / Plasmid: pET13a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)RIL / References: UniProt: P21673, diamine N-acetyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: mmPEG500, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 28155 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.85→30 Å / σ(F): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.24 1404 random
Rwork0.21 --
all0.21 28155 -
obs0.21 26751 -
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 10 157 2848

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