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- PDB-1l0c: Investigation of the Roles of Catalytic Residues in Serotonin N-A... -

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Basic information

Entry
Database: PDB / ID: 1l0c
TitleInvestigation of the Roles of Catalytic Residues in Serotonin N-Acetyltransferase
ComponentsSerotonin N-acetyltransferase
KeywordsTRANSFERASE / Enzyme-inhibitor complex / bisubstrate analog / alternate conformations
Function / homology
Function and homology information


melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / aralkylamine N-acetyltransferase / N-terminal protein amino acid acetylation / response to light stimulus / 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 TRYPTAMINE / Serotonin N-acetyltransferase
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsScheibner, K.A. / De Angelis, J. / Burley, S.K. / Cole, P.A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Investigation of the roles of catalytic residues in serotonin N-acetyltransferase.
Authors: Scheibner, K.A. / De Angelis, J. / Burley, S.K. / Cole, P.A.
History
DepositionFeb 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 24, 2011Group: Atomic model
Revision 1.4Feb 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 1.5Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)24,0632
Polymers23,0961
Non-polymers9681
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.210, 68.681, 89.422
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 / AA-NAT / SEROTONIN ACETYLASE


Mass: 23095.568 Da / Num. of mol.: 1 / Mutation: Y168F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Gene: AANAT / 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-COT / COA-S-ACETYL TRYPTAMINE


Mass: 967.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H48N9O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 2000, MPD, MES pH 6.5, ammonium acetate, magnesium acetate, lithium chloride, spermidine, DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Details: Wolf, E., (2002) J. Mol. Biol., 317, 215., 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: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2000
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 7822 / Num. obs: 7188 / % possible obs: 91.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 25.2
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 14.1 / Num. unique all: 497 / Rsym value: 0.092 / % possible all: 93
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 75910 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 93 % / Rmerge(I) obs: 0.092

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KUV

1kuv


Resolution: 2.3→20 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. reflectionSelection details
Rfree0.2464 740 RANDOM
Rwork0.1927 --
all0.1877 7485 -
obs0.1877 6912 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.48 Å20 Å20 Å2
2---11.297 Å20 Å2
3---3.818 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 63 90 1464
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_mcbond_it1.3
X-RAY DIFFRACTIONc_mcangle_it1.9
X-RAY DIFFRACTIONc_scangle_it2.8
X-RAY DIFFRACTIONc_scbond_it1.9
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.1877 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS

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