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- PDB-1kux: X-ray Crystallographic Studies of Serotonin N-acetyltransferase C... -

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Basic information

Entry
Database: PDB / ID: 1kux
TitleX-ray Crystallographic Studies of Serotonin N-acetyltransferase Catalysis and Inhibition
ComponentsSerotonin N-acetyltransferaseAralkylamine N-acetyltransferase
KeywordsTRANSFERASE / Enzyme-Inhibitor Complex / Bisubstrate Analog / Alternate Conformations
Function / homology
Function and homology information


aralkylamine N-acetyltransferase / melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / N-terminal protein amino acid acetylation / cellular response to cAMP / circadian rhythm / perinuclear region of cytoplasm
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
COA-S-TRIMETHYLENE-ACETYL-TRYPTAMINE / Serotonin N-acetyltransferase
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWolf, E. / De Angelis, J. / Khalil, E.M. / Cole, P.A. / Burley, S.K.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: X-ray crystallographic studies of serotonin N-acetyltransferase catalysis and inhibition.
Authors: Wolf, E. / De Angelis, J. / Khalil, E.M. / Cole, P.A. / Burley, S.K.
History
DepositionJan 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serotonin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1212
Polymers23,1121
Non-polymers1,0101
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.455, 68.567, 89.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a monomer

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Components

#1: Protein Serotonin N-acetyltransferase / Aralkylamine N-acetyltransferase / E.C.2.3.1.87 / arylalkylamine N-acetyltransferase / Aralkylamine N-acetyltransferase / AA-NAT / Serotonin acetylase


Mass: 23111.568 Da / Num. of mol.: 1 / Mutation: MET substituted by Se-met
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Gene: U29663 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q29495, aralkylamine N-acetyltransferase
#2: Chemical ChemComp-CA3 / COA-S-TRIMETHYLENE-ACETYL-TRYPTAMINE


Mass: 1009.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H54N9O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 2000, MPD, ammonium sulfate, MES pH 6.5, magnesium acetate, DTT, spermidine, and lithium chloride. pH 6.5, VAPOR DIFFUSION, HANGING DROP at 277K, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMMES1reservoirpH6.5
230 %(w/v)PEG20001reservoir
30.2 Mammonium acetate1reservoir
40.1 Mmagnesium acetate1reservoir
52.0 %(v/v)MPD1reservoir
630 mMdithiothreitol1reservoir
720 mMspermidine1reservoir
80.1 M1reservoirLiCl
97 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 20, 2000
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 13976 / Num. obs: 13920 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 25.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 7.3 / Num. unique all: 1375 / Rsym value: 0.16 / % possible all: 97.8
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 25 Å
Reflection shell
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KUV

1kuv


Resolution: 1.8→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Structure was refined with waters and ligand was modeled based on difference fourier electron density. Ligand was included in final refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1343 -RANDOM
Rwork0.197 ---
all0.2 13976 --
obs0.2 13680 87.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.776 Å20 Å20 Å2
2---2.246 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 66 160 1538
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_mcbond_it1.24
X-RAY DIFFRACTIONc_mcangle_it1.85
X-RAY DIFFRACTIONc_scbond_it2.01
X-RAY DIFFRACTIONc_scangle_it2.89
Refinement
*PLUS
Rfactor obs: 0.197 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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