[English] 日本語
Yorodumi
- PDB-5gif: Crystal Structure of Drosophila melanogaster E47D Dopamine N-Acet... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gif
TitleCrystal Structure of Drosophila melanogaster E47D Dopamine N-Acetyltransferase in Binary Complex with Acetyl-CoA
ComponentsDopamine N-acetyltransferase
KeywordsTRANSFERASE / Dopamine N-acetyltransferase(Dat) / GCN5-related N-acetyltransferase(GNAT) / Arylalkylamine N-acetyltransferase(AANAT) / Order bi-bi sequential mechanism
Function / homology
Function and homology information


chitin-based cuticle sclerotization / serotonin catabolic process / octopamine catabolic process / aralkylamine N-acetyltransferase / melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / arylamine N-acetyltransferase activity / regulation of circadian sleep/wake cycle, sleep / catecholamine metabolic process / dopamine catabolic process ...chitin-based cuticle sclerotization / serotonin catabolic process / octopamine catabolic process / aralkylamine N-acetyltransferase / melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / arylamine N-acetyltransferase activity / regulation of circadian sleep/wake cycle, sleep / catecholamine metabolic process / dopamine catabolic process / sleep / N-acetyltransferase activity / nucleus / 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
ACETYL COENZYME *A / (4S,5S)-1,2-DITHIANE-4,5-DIOL / Arylalkylamine N-acetyltransferase 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsYang, Y.C. / Wu, C.Y. / Cheng, H.C. / Lyu, P.C.
CitationJournal: To Be Published
Title: Crystal Structure of Drosophila melanogaster E47D Dopamine N-Acetyltransferase in Binary Complex with Acetyl-CoA
Authors: Yang, Y.C. / Wu, C.Y. / Cheng, H.C. / Lyu, P.C.
History
DepositionJun 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dopamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5424
Polymers24,4281
Non-polymers1,1143
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.138, 56.580, 84.203
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Dopamine N-acetyltransferase / Arylalkylamine N-acetyltransferase / aaNAT1


Mass: 24428.023 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 56-265 / Mutation: E47D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dat, NAT1, CG3318 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12
References: UniProt: Q94521, aralkylamine N-acetyltransferase
#2: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1.0M NaH2PO4/1.6M K2HPO4, 0.1M Imidazole, 0.2M NaCl
PH range: 6.5-7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.29→30 Å / Num. obs: 53391 / % possible obs: 99 % / Redundancy: 7.4 % / Biso Wilson estimate: 12.36 Å2 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.019 / Rrim(I) all: 0.052 / Χ2: 0.987 / Net I/av σ(I): 38.63 / Net I/σ(I): 15 / Num. measured all: 397598
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.29-1.346.40.422190.3
1.34-1.397.60.3541100
1.39-1.457.80.2691100
1.45-1.537.70.1861100
1.53-1.637.70.1281100
1.63-1.757.70.0921100
1.75-1.937.60.0621100
1.93-2.217.40.0511100
2.21-2.787.30.046199.9
2.78-307.20.03199.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.44 Å26.82 Å
Translation5.44 Å26.82 Å

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.2phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→26.824 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.62
RfactorNum. reflection% reflection
Rfree0.1856 2630 5 %
Rwork0.1514 --
obs0.1531 52562 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 40.79 Å2 / Biso mean: 16.99 Å2 / Biso min: 7.44 Å2
Refinement stepCycle: final / Resolution: 1.3→26.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 67 281 2035
Biso mean--14.62 26.76 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061796
X-RAY DIFFRACTIONf_angle_d1.2592430
X-RAY DIFFRACTIONf_chiral_restr0.08258
X-RAY DIFFRACTIONf_plane_restr0.006308
X-RAY DIFFRACTIONf_dihedral_angle_d15.501694
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.32360.25061350.172625632698100
1.3236-1.34910.24641370.156426082745100
1.3491-1.37660.17241370.138226032740100
1.3766-1.40660.17391350.124225712706100
1.4066-1.43930.15821390.121526212760100
1.4393-1.47530.19031360.127625912727100
1.4753-1.51520.15861370.123126122749100
1.5152-1.55970.17461380.114426112749100
1.5597-1.61010.16481360.115625852721100
1.6101-1.66760.18041390.122526272766100
1.6676-1.73440.17471350.126325782713100
1.7344-1.81330.17221390.132326452784100
1.8133-1.90890.18761390.142226292768100
1.9089-2.02840.18951380.138426262764100
2.0284-2.1850.16651390.138726422781100
2.185-2.40470.16921400.153126572797100
2.4047-2.75240.19951410.177826702811100
2.7524-3.46660.21311420.176226932835100
3.4666-26.82930.18041480.1682800294899

+
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