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- PDB-5gi6: Crystal Structure of Drosophila melanogaster Dopamine N-Acetyltra... -

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Basic information

Entry
Database: PDB / ID: 5gi6
TitleCrystal Structure of Drosophila melanogaster Dopamine N-Acetyltransferase Bound to CoA and Phenylethylamine
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 / melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / aralkylamine N-acetyltransferase / arylamine N-acetyltransferase activity / regulation of circadian sleep/wake cycle, sleep / catecholamine metabolic process / N-acetyltransferase activity ...chitin-based cuticle sclerotization / serotonin catabolic process / octopamine catabolic process / melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / aralkylamine N-acetyltransferase / arylamine N-acetyltransferase activity / regulation of circadian sleep/wake cycle, sleep / catecholamine metabolic process / N-acetyltransferase activity / dopamine catabolic process / sleep / nucleus / cytoplasm
Similarity search - Function
Acetyltransferase (GNAT) domain / 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
COENZYME A / 2-PHENYLETHYLAMINE / Arylalkylamine N-acetyltransferase 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsYang, Y.C. / Cheng, H.C. / Lyu, P.C.
CitationJournal: To Be Published
Title: Crystal Structure of Drosophila melanogaster Dopamine N-Acetyltransferase Bound to CoA and Phenylethylamine
Authors: Yang, Y.C. / Cheng, H.C. / Lyu, P.C.
History
DepositionJun 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dopamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3323
Polymers24,4421
Non-polymers8902
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.688, 48.536, 89.480
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 Dopamine N-acetyltransferase / Arylalkylamine N-acetyltransferase / aaNAT1


Mass: 24442.049 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 56-265
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-PEA / 2-PHENYLETHYLAMINE


Mass: 122.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.12 Å3/Da / Density % sol: 41.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0M NaH2PO4/1.6M K2HPO4, 0.1M Imidazole, 0.2M NaCl
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 26434 / % possible obs: 96.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.24 Å2 / Rmerge(I) obs: 0.048 / Net I/av σ(I): 31.628 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.6-1.666.30.614193
1.66-1.726.30.43193.3
1.72-1.86.30.302193.4
1.8-1.96.30.206193.8
1.9-2.026.20.143194.4
2.02-2.176.10.103196.9
2.17-2.396.10.075199.1
2.39-2.746.20.054198.8
2.74-3.4570.039199.8
3.45-306.60.031198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.41 Å25.29 Å
Translation5.41 Å25.29 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→25.288 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.7
RfactorNum. reflection% reflection
Rfree0.2124 1231 4.97 %
Rwork0.1865 --
obs0.1878 24777 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.42 Å2 / Biso mean: 33.11 Å2 / Biso min: 15.77 Å2
Refinement stepCycle: final / Resolution: 1.65→25.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1626 0 57 145 1828
Biso mean--24.67 38.41 -
Num. residues----202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071723
X-RAY DIFFRACTIONf_angle_d1.2122328
X-RAY DIFFRACTIONf_chiral_restr0.079244
X-RAY DIFFRACTIONf_plane_restr0.006296
X-RAY DIFFRACTIONf_dihedral_angle_d16.23663
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.71610.29551310.2262476260793
1.7161-1.79410.23751260.21362502262894
1.7941-1.88870.25771360.19842500263694
1.8887-2.0070.22381340.18932529266394
2.007-2.16190.18331320.1822598273097
2.1619-2.37930.23591370.19042668280599
2.3793-2.72320.23291430.20162684282799
2.7232-3.42960.22151440.191127442888100
3.4296-25.29080.18351480.17092845299399
Refinement TLS params.Method: refined / Origin x: 1.7848 Å / Origin y: -19.1016 Å / Origin z: -8.9811 Å
111213212223313233
T0.1802 Å20.0033 Å2-0.0092 Å2-0.1469 Å20.0584 Å2--0.2262 Å2
L3.2609 °21.0239 °2-0.2952 °2-1.3708 °2-0.1851 °2--1.4842 °2
S0.0337 Å °-0.1623 Å °-0.5503 Å °-0.0248 Å °-0.0997 Å °-0.2022 Å °0.0877 Å °-0.0274 Å °-0.048 Å °
Refinement TLS groupSelection details: ALL

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