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- PDB-2g3t: Crystal structure of human spermidine/spermine N1-acetyltransfera... -

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Basic information

Entry
Database: PDB / ID: 2g3t
TitleCrystal structure of human spermidine/spermine N1-acetyltransferase (hSSAT)
ComponentsDiamine acetyltransferase 1
KeywordsTRANSFERASE / alpha / beta fold
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
Diamine acetyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZhu, Y.Q. / Yang, N. / Wang, D.C.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of human spermidine/spermine N1-acetyltransferase (hSSAT): the first structure of a new sequence family of transferase homologous superfamily
Authors: Zhu, Y.Q. / Zhu, D.Y. / Yin, L. / Zhang, Y. / Vonrhein, C. / Wang, D.C.
History
DepositionFeb 21, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 23, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.5Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)42,2382
Polymers42,2382
Non-polymers00
Water6,431357
1
A: Diamine acetyltransferase 1

A: Diamine acetyltransferase 1


Theoretical massNumber of molelcules
Total (without water)42,2382
Polymers42,2382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7220 Å2
ΔGint-58.7 kcal/mol
Surface area16410 Å2
MethodPISA
2
B: Diamine acetyltransferase 1

B: Diamine acetyltransferase 1


Theoretical massNumber of molelcules
Total (without water)42,2382
Polymers42,2382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7240 Å2
ΔGint-59 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.430, 65.666, 181.065
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-327-

HOH

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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 / hSSAT


Mass: 21119.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P21673, diamine N-acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M TrisHCl pH8.0, 2.8M NaCl, 0.2M NaK Tartrate, 0.05MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
2951
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
ROTATING ANODERIGAKU MICROMAX-00722.29
Detector
TypeIDDetectorDate
RIGAKU1IMAGE PLATEDec 8, 2005
RIGAKU RAXIS IV2IMAGE PLATENov 4, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.291
ReflectionResolution: 1.79→50 Å / Num. all: 37112 / Num. obs: 37066 / % possible obs: 99.88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.79→1.85 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
OASISmodel building
CNS1.1refinement
HKL-2000data reduction
OASISV. 2004phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 3551 9.7 %random
Rwork0.2273 ---
obs0.2273 35574 97.2 %-
all-36606 --
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 0 357 3102

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