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- PDB-7dai: The crystal structure of a serotonin N-acetyltransferase from Ory... -

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Basic information

Entry
Database: PDB / ID: 7dai
TitleThe crystal structure of a serotonin N-acetyltransferase 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
Serotonin N-acetyltransferase 1, chloroplastic
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
C: Serotonin N-acetyltransferase 1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)55,5213
Polymers55,5213
Non-polymers00
Water59433
1
A: Serotonin N-acetyltransferase 1, chloroplastic

A: Serotonin N-acetyltransferase 1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)37,0142
Polymers37,0142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4680 Å2
ΔGint-33 kcal/mol
Surface area13850 Å2
MethodPISA
2
B: Serotonin N-acetyltransferase 1, chloroplastic
C: Serotonin N-acetyltransferase 1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)37,0142
Polymers37,0142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-30 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.703, 77.550, 110.438
Angle α, β, γ (deg.)90.000, 110.500, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

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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.: 3
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 4 Å3/Da / Density % sol: 69.24 %
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: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.3→19.97 Å / Num. obs: 38989 / % possible obs: 98.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 49.26 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.039 / Rrim(I) all: 0.1 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3819 / CC1/2: 0.922 / Rpim(I) all: 0.245 / Rrim(I) all: 0.641 / % 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: 2.3→19.969 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2837 1649 4.23 %
Rwork0.2368 37295 -
obs0.2388 38944 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.71 Å2 / Biso mean: 56.5928 Å2 / Biso min: 32.13 Å2
Refinement stepCycle: final / Resolution: 2.3→19.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 0 33 3519
Biso mean---54.07 -
Num. residues----440
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.36760.3291370.27523084100
2.3676-2.44390.3491360.26983082100
2.4439-2.53110.28751370.2698307399
2.5311-2.63220.32991380.25853118100
2.6322-2.75170.311370.24993088100
2.7517-2.89640.29561350.26363081100
2.8964-3.07720.34551380.25313145100
3.0772-3.31380.32831360.25393058100
3.3138-3.64550.26971380.24493124100
3.6455-4.16880.26531380.21573119100
4.1688-5.23650.2361380.20263139100
5.2365-19.9690.28491410.24543184100

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