[English] 日本語
Yorodumi
- PDB-1kux: X-ray Crystallographic Studies of Serotonin N-acetyltransferase C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kux
TitleX-ray Crystallographic Studies of Serotonin N-acetyltransferase Catalysis and Inhibition
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-TRIMETHYLENE-ACETYL-TRYPTAMINE / Serotonin N-acetyltransferase
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.3Feb 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 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serotonin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1212
Polymers23,1121
Non-polymers1,0101
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.455, 68.567, 89.791
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

-
Components

#1: Protein Serotonin 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-CA3 / COA-S-TRIMETHYLENE-ACETYL-TRYPTAMINE


Mass: 1009.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H54N9O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.9 %
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. pH 6.5, 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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 20, 2000
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 13976 / Num. obs: 13920 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 25.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 7.3 / Num. unique all: 1375 / Rsym value: 0.16 / % possible all: 97.8
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 25 Å
Reflection shell
*PLUS
% possible obs: 97.8 %

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KUV

1kuv


Resolution: 1.8→25 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. reflection% reflectionSelection details
Rfree0.225 1343 -RANDOM
Rwork0.197 ---
all0.2 13976 --
obs0.2 13680 87.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.776 Å20 Å20 Å2
2---2.246 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 66 160 1538
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_mcbond_it1.24
X-RAY DIFFRACTIONc_mcangle_it1.85
X-RAY DIFFRACTIONc_scbond_it2.01
X-RAY DIFFRACTIONc_scangle_it2.89
Refinement
*PLUS
Rfactor obs: 0.197 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more