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- PDB-2b3v: Spermine spermidine acetyltransferase in complex with acetylcoa, ... -

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Basic information

Entry
Database: PDB / ID: 2b3v
TitleSpermine spermidine acetyltransferase in complex with acetylcoa, K26R mutant
ComponentsDiamine acetyltransferase 1
KeywordsTRANSFERASE / polyamine / 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 / 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
ACETYL COENZYME *A / Diamine acetyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 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: Derived calculations / 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 1.5Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2142
Polymers20,4041
Non-polymers8101
Water1,06359
1
A: Diamine acetyltransferase 1
hetero molecules

A: Diamine acetyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4284
Polymers40,8092
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_675-x+1,-y+2,z1
Buried area9350 Å2
ΔGint-67 kcal/mol
Surface area16660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.994, 62.994, 80.909
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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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.: 1 / 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) / References: UniProt: P21673, diamine N-acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: mmPEG5000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.98 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 12884 / % possible obs: 96.6 % / 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: 1.95→30 Å / σ(F): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.257 651 random
Rwork0.222 --
obs-12884 -
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 51 59 1490

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