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

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Basic information

Entry
Database: PDB / ID: 1kuv
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-ACETYL 5-BROMOTRYPTAMINE / Serotonin N-acetyltransferase
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Feb 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 1.6Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)24,1833
Polymers23,1121
Non-polymers1,0712
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.313, 68.716, 89.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1027-

HOH

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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA5 / COA-S-ACETYL 5-BROMOTRYPTAMINE


Mass: 1046.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H47BrN9O17P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.78 Å3/Da / Density % sol: 30.81 %
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. 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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.97946, 0.97927, 0.92011, 0.91970
SYNCHROTRONCHESS F120.91
Detector
TypeIDDetectorDate
BRANDEIS - B41CCDMar 23, 1999
ADSC QUANTUM 42CCDJan 6, 1999
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111MADMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
20.979271
30.920111
40.91971
50.911
ReflectionResolution: 2→25 Å / Num. all: 11494 / Num. obs: 10517 / % possible obs: 91.5 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 16.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 9.6 / Num. unique all: 1148 / Rsym value: 0.123 / % possible all: 79.5
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 25 Å / % possible obs: 92 % / Num. measured all: 86780
Reflection shell
*PLUS
% possible obs: 80 %

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Processing

Software
NameVersionClassification
SnBphasing
MLPHAREphasing
DMmodel building
CNS1refinement
MARMADdata reduction
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Structure was solved based on MAD data collected in the vicinity of the bromine and selenium edges. Ligand density was identified by difference fourier. The final model (protein and ligand) ...Details: Structure was solved based on MAD data collected in the vicinity of the bromine and selenium edges. Ligand density was identified by difference fourier. The final model (protein and ligand) was refined at 2.0 Angstrom
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1055 10 %RANDOM
Rwork0.203 ---
all0.226 11474 --
obs0.226 10402 90.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.943 Å20 Å20 Å2
2---13.236 Å20 Å2
3---6.293 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 129 167 1608
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_mcbond_it1.27
X-RAY DIFFRACTIONc_mcangle_it1.89
X-RAY DIFFRACTIONc_scbond_it1.94
X-RAY DIFFRACTIONc_scangle_it2.95
Refinement
*PLUS
Lowest resolution: 25 Å / Num. reflection obs: 10057 / % reflection Rfree: 10 % / Rfactor obs: 0.203 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS

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