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- PDB-6k5m: The crystal structure of a serotonin N-acetyltransferase from Ory... -

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Basic information

Entry
Database: PDB / ID: 6k5m
TitleThe crystal structure of a serotonin N-acetyltransferase from Oryza Sativa (Rice)
ComponentsSerotonin N-acetyltransferase 1, chloroplastic
KeywordsTRANSFERASE / serotonin 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 / aralkylamine N-acetyltransferase activity / 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 / serotonin metabolic process / response to hydrogen sulfide / 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 / SAD / Resolution: 1.793 Å
AuthorsZhou, Y.Z. / Liao, L.J. / Liu, X.K. / Guo, Y. / Zhao, Y.C. / Zeng, Z.X.
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
DepositionMay 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serotonin N-acetyltransferase 1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)19,5151
Polymers19,5151
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9450 Å2
Unit cell
Length a, b, c (Å)66.893, 66.893, 82.692
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

21A-370-

HOH

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Components

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


Mass: 19514.594 Da / Num. of mol.: 1
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) / Strain (production host): BL21(DE3)
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.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / Details: 2M MgCl2, 18% PEG8000, Tris-HCl, PH8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2017
RadiationMonochromator: Se / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 18235 / % possible obs: 100 % / Redundancy: 24.9 % / Biso Wilson estimate: 35.14 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 67.435
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 26.3 % / Rmerge(I) obs: 0.857 / Num. unique obs: 1781 / CC1/2: 0.903 / Rsym value: 0.857 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.793→41.058 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.11
RfactorNum. reflection% reflection
Rfree0.2342 1819 10 %
Rwork0.2247 --
obs0.2256 18186 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.74 Å2 / Biso mean: 40.8758 Å2 / Biso min: 20.45 Å2
Refinement stepCycle: final / Resolution: 1.793→41.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 0 81 1331
Biso mean---44.08 -
Num. residues----155
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7928-1.84130.34051340.281205133998
1.8413-1.89550.31071370.282912341371100
1.8955-1.95660.32031360.267112261362100
1.9566-2.02660.25621390.243912581397100
2.0266-2.10770.26921370.238512201357100
2.1077-2.20360.27361380.241912441382100
2.2036-2.31980.26361380.236112501388100
2.3198-2.46510.26631390.239212451384100
2.4651-2.65540.24831400.246112611401100
2.6554-2.92260.24331400.234412621402100
2.9226-3.34530.26811430.227212801423100
3.3453-4.21410.20071430.210412981441100
4.2141-41.06880.20041550.206313841539100

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