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- PDB-6k80: Crystal Structure of Drosophila melanogaster Dopamine N-Acetyltra... -

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Basic information

Entry
Database: PDB / ID: 6k80
TitleCrystal Structure of Drosophila melanogaster Dopamine N-Acetyltransferase in Complex with CoA and Tryptophol
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 / 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 / 2-(1H-indol-3-yl)ethanol / Arylalkylamine N-acetyltransferase 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsWu, C.Y. / Hu, I.C. / Yang, Y.C. / Cheng, H.C. / Lyu, P.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)106-2311-B-007-004-MY3 Taiwan
CitationJournal: Commun Biol / Year: 2020
Title: An essential role of acetyl coenzyme A in the catalytic cycle of insect arylalkylamine N-acetyltransferase.
Authors: Wu, C.Y. / Hu, I.C. / Yang, Y.C. / Ding, W.C. / Lai, C.H. / Lee, Y.Z. / Liu, Y.C. / Cheng, H.C. / Lyu, P.C.
History
DepositionJun 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2Nov 22, 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

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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)25,7375
Polymers24,4441
Non-polymers1,2934
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-2 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.636, 56.447, 84.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 24444.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: AANAT1, Dat, NAT1, CG3318
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q94521, aralkylamine N-acetyltransferase
#2: Chemical ChemComp-ZCW / 2-(1H-indol-3-yl)ethanol


Mass: 161.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H11NO
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


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


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.91 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.28→30 Å / Num. obs: 54084 / % possible obs: 99.5 % / Redundancy: 7.5 % / Biso Wilson estimate: 12.13 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.052 / Χ2: 1.056 / Net I/σ(I): 39.18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.28-1.335.30.51451240.8440.230.5660.97295.8
1.33-1.387.30.4353480.9210.1680.4621.02199.7
1.38-1.447.90.32253410.960.1220.3441.05100
1.44-1.527.90.22553870.9790.0850.2411.074100
1.52-1.617.90.14953840.9910.0560.1591.048100
1.61-1.7480.10754110.9950.040.1151.102100
1.74-1.917.90.07254000.9980.0270.0771.006100
1.91-2.197.70.06254640.9970.0240.0661.032100
2.19-2.767.60.04655090.9980.0180.0491.085100
2.76-307.70.024571610.0090.0251.13299.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
MOLREP6.5phasing
PHENIX1.13-2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TE4

3te4


Resolution: 1.28→26.76 Å / SU ML: 0.1063 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.0359
RfactorNum. reflection% reflection
Rfree0.1986 2694 4.99 %
Rwork0.1849 --
obs0.1856 54013 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.68 Å2
Refinement stepCycle: final / Resolution: 1.28→26.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 0 87 261 2060
Biso mean--14.29 23.76 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591845
X-RAY DIFFRACTIONf_angle_d1.22952496
X-RAY DIFFRACTIONf_chiral_restr0.0871257
X-RAY DIFFRACTIONf_plane_restr0.0063317
X-RAY DIFFRACTIONf_dihedral_angle_d7.4996686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.30.28781140.24912463X-RAY DIFFRACTION91.84
1.3-1.330.25111250.22892638X-RAY DIFFRACTION97.84
1.33-1.350.25351500.21712647X-RAY DIFFRACTION99.54
1.35-1.380.21051560.20542658X-RAY DIFFRACTION100
1.38-1.420.21111470.19672688X-RAY DIFFRACTION100
1.42-1.450.23381240.19772718X-RAY DIFFRACTION100
1.45-1.490.18271370.18822693X-RAY DIFFRACTION100
1.49-1.530.2191420.18272688X-RAY DIFFRACTION99.96
1.53-1.580.19811450.17542680X-RAY DIFFRACTION99.96
1.58-1.640.18161400.17642696X-RAY DIFFRACTION100
1.64-1.710.19291530.17732695X-RAY DIFFRACTION100
1.71-1.780.19211380.18182715X-RAY DIFFRACTION99.96
1.78-1.880.18361430.1862707X-RAY DIFFRACTION100
1.88-20.20751330.18022737X-RAY DIFFRACTION100
2-2.150.18291410.1762730X-RAY DIFFRACTION100
2.15-2.370.19891410.18352740X-RAY DIFFRACTION100
2.37-2.710.2271470.19512758X-RAY DIFFRACTION99.97
2.71-3.410.22021450.19312783X-RAY DIFFRACTION99.93
3.41-26.760.16941730.16842885X-RAY DIFFRACTION99.38

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