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- PDB-2b4d: SSAT+COA+SP- SP disordered -

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Basic information

Entry
Database: PDB / ID: 2b4d
TitleSSAT+COA+SP- SP disordered
Components(Diamine acetyltransferase 1) x 2
KeywordsTRANSFERASE / 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
COENZYME A / Diamine acetyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 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.S. / Matz, E. / Studier, F.W. / Pegg, A.P. / Coleman, C.S. / Flanagan, J.M.
History
DepositionSep 23, 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 1.3Feb 3, 2021Group: Advisory / Derived calculations / Structure summary
Category: audit_author / pdbx_unobs_or_zero_occ_atoms ...audit_author / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)42,3294
Polymers40,7942
Non-polymers1,5352
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-62 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.005, 74.005, 64.015
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 20376.254 Da / Num. of mol.: 1
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: Protein Diamine acetyltransferase 1


Mass: 20417.283 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.15 Å3/Da / Density % sol: 42.79 %

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 23463 / Num. obs: 22575

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / σ(F): -3
RfactorNum. reflection% reflection
Rwork0.221 --
Rfree-1127 0.256 %
all-23463 -
obs-22575 -
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 96 75 2976

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