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- PDB-5gi8: Crystal Structure of Drosophila melanogaster Dopamine N-Acetyltra... -

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Basic information

Entry
Database: PDB / ID: 5gi8
TitleCrystal Structure of Drosophila melanogaster Dopamine N-Acetyltransferase in Ternary Complex with CoA and Acetyl-dopamine
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 / N-acetyltransferase activity ...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 / 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
~{N}-[2-[3,4-bis(oxidanyl)phenyl]ethyl]ethanamide / 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. / Lin, S.J. / Cheng, K.C. / Cheng, H.C. / Lyu, P.C.
CitationJournal: To Be Published
Title: Crystal Structure of Drosophila melanogaster Dopamine N-Acetyltransferase in Ternary Complex with CoA and Acetyl-dopamine
Authors: Yang, Y.C. / Lin, S.J. / Cheng, K.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)25,5574
Polymers24,4421
Non-polymers1,1153
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.039, 56.500, 83.644
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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-7DP / ~{N}-[2-[3,4-bis(oxidanyl)phenyl]ethyl]ethanamide / N-acetyldopamine


Mass: 195.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO3
#4: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
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: 1.03964 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03964 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 52082 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 13.31 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Χ2: 0.819 / Net I/av σ(I): 30.871 / Net I/σ(I): 11.5 / Num. measured all: 351582
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.3-1.355.90.58551050.8210.2580.6410.57199.5
1.35-1.46.80.46851240.90.1940.5070.618100
1.4-1.466.80.33251560.9460.1370.3590.654100
1.46-1.546.90.22451450.9730.0920.2420.731100
1.54-1.646.90.14951800.9890.0610.1610.79100
1.64-1.7670.10151930.9950.0410.1090.832100
1.76-1.9470.06951890.9970.0280.0751.059100
1.94-2.226.80.05552330.9970.0230.061.004100
2.22-2.86.70.0452720.9990.0170.0430.96599.9
2.8-306.70.03354850.9990.0140.0360.90599.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.47 Å23.78 Å
Translation5.47 Å23.78 Å

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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→23.778 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.42
RfactorNum. reflection% reflection
Rfree0.1847 2600 5 %
Rwork0.1516 --
obs0.1532 52016 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 42.57 Å2 / Biso mean: 17.18 Å2 / Biso min: 7.7 Å2
Refinement stepCycle: final / Resolution: 1.3→23.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 70 227 1985
Biso mean--11.18 26.3 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061800
X-RAY DIFFRACTIONf_angle_d1.2432435
X-RAY DIFFRACTIONf_chiral_restr0.077256
X-RAY DIFFRACTIONf_plane_restr0.006310
X-RAY DIFFRACTIONf_dihedral_angle_d16.25693
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 (%)
1.2997-1.32330.26931310.22422486261798
1.3233-1.34880.22351370.180525952732100
1.3488-1.37630.17521350.15425812716100
1.3763-1.40620.17761340.135725382672100
1.4062-1.43890.20761350.138625712706100
1.4389-1.47490.16721360.134525722708100
1.4749-1.51480.16371360.124725862722100
1.5148-1.55940.17541360.10925852721100
1.5594-1.60970.15381350.108925792714100
1.6097-1.66720.1631370.112825922729100
1.6672-1.73390.15941350.117325902725100
1.7339-1.81280.15271370.126825942731100
1.8128-1.90840.17091370.136326012738100
1.9084-2.02790.19021360.138426032739100
2.0279-2.18430.17411380.137426112749100
2.1843-2.4040.17211380.15126332771100
2.404-2.75140.17251400.173226582798100
2.7514-3.46470.22261400.177326652805100
3.4647-23.78220.19321470.16632776292399

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