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- PDB-7dal: The crystal structure of a serotonin N-acetyltransferase in compl... -

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Basic information

Entry
Database: PDB / ID: 7dal
TitleThe crystal structure of a serotonin N-acetyltransferase in complex with serotonin and acetyl-CoA from Oryza Sativa
ComponentsSerotonin N-acetyltransferase 1, chloroplastic
KeywordsTRANSFERASE / N-acetyltransferase
Function / homology
Function and homology information


transport of virus in multicellular host / mucilage biosynthetic process involved in seed coat development / photosynthetic state transition / seed oilbody biogenesis / regulation of starch metabolic process / response to mannitol / regulation of anthocyanin metabolic process / thylakoid membrane organization / negative regulation of seed germination / melatonin biosynthetic process ...transport of virus in multicellular host / mucilage biosynthetic process involved in seed coat development / photosynthetic state transition / seed oilbody biogenesis / regulation of starch metabolic process / response to mannitol / regulation of anthocyanin metabolic process / thylakoid membrane organization / negative regulation of seed germination / melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / aralkylamine N-acetyltransferase / regulation of photoperiodism, flowering / regulation of stomatal closure / response to high light intensity / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / N-acetyltransferase activity / response to hydrogen sulfide / serotonin metabolic process / response to osmotic stress / protein quality control for misfolded or incompletely synthesized proteins / defense response to fungus / response to cold / chloroplast / circadian rhythm / nucleus / cytoplasm
Similarity search - Function
Acetyltransferase NSI-like / 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
ACETYL COENZYME *A / SEROTONIN / Serotonin N-acetyltransferase 1, chloroplastic
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhou, Y.Z. / Liao, L.J. / Tang, T. / Guo, Y. / Liu, X.K. / Liu, B. / Zhao, Y.C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structural and Molecular Dynamics Analysis of Plant Serotonin N-Acetyltransferase Reveal an Acid/Base-Assisted Catalysis in Melatonin Biosynthesis.
Authors: Liao, L. / Zhou, Y. / Xu, Y. / Zhang, Y. / Liu, X. / Liu, B. / Chen, X. / Guo, Y. / Zeng, Z. / Zhao, Y.
History
DepositionOct 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Serotonin N-acetyltransferase 1, chloroplastic
B: Serotonin N-acetyltransferase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9866
Polymers37,0142
Non-polymers1,9724
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-39 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.551, 66.803, 81.917
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serotonin N-acetyltransferase 1, chloroplastic / OsSNAT1 / Nuclear shuttle protein-interacting protein homolog / Probable acetyltransferase NSI


Mass: 18507.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: SNAT1, GNAT5, NSI, SNAT, Os05g0481000, LOC_Os05g40260, OsJ_018182, OsJ_18949, OSJNBa0095J22.4
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5KQI6, aralkylamine N-acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL


Mass: 176.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H12N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% (w/v) Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979183 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.5→19.58 Å / Num. obs: 12345 / % possible obs: 93.6 % / Redundancy: 12.5 % / Biso Wilson estimate: 65.17 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.017 / Rrim(I) all: 0.059 / Net I/σ(I): 12.5
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 13.4 / Num. unique obs: 1458 / Rpim(I) all: 0.179 / Rrim(I) all: 0.661 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IV7

6iv7


Resolution: 2.5→19.58 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2692 617 5.02 %
Rwork0.2271 11684 -
obs0.2293 12301 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.21 Å2 / Biso mean: 73.6268 Å2 / Biso min: 46.79 Å2
Refinement stepCycle: final / Resolution: 2.5→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 128 1 2453
Biso mean--87.71 50.3 -
Num. residues----292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5003-2.75130.30751220.3054227875
2.7513-3.1480.32881500.28213096100
3.148-3.96080.29391780.2393073100
3.9608-19.580.23931670.20343237100

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