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- PDB-8wmb: Crystal Structure of Drosophila melanogaster D46A Dopamine N-Acet... -

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Basic information

Entry
Database: PDB / ID: 8wmb
TitleCrystal Structure of Drosophila melanogaster D46A Dopamine N-Acetyltransferase in Complex with Acetyl-CoA
ComponentsArylalkylamine N-acetyltransferase 1
KeywordsTRANSFERASE / Dopamine N-acetyltransferase(Dat) / GCN5-related N-acetyltransferase(GNAT) / Arylalkylamine N-acetyltransferase(AANAT)
Function / homology
Function and homology information


chitin-based cuticle sclerotization / serotonin catabolic process / octopamine catabolic process / melatonin biosynthetic process / aralkylamine N-acetyltransferase / 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 / melatonin biosynthetic process / aralkylamine N-acetyltransferase / 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) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / Arylalkylamine N-acetyltransferase 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.645 Å
AuthorsWu, C.Y. / Hu, I.C. / Cheng, H.C. / Lyu, P.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)106-2311-B-007-004-MY3 Taiwan
CitationJournal: To Be Published
Title: Crystal Structure of Drosophila melanogaster D46A Dopamine N-Acetyltransferase in Complex with Acetyl-CoA
Authors: Wu, C.Y. / Hu, I.C. / Cheng, H.C. / Lyu, P.C.
History
DepositionOct 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arylalkylamine N-acetyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2102
Polymers24,4001
Non-polymers8101
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-4 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.948, 53.162, 85.754
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Arylalkylamine N-acetyltransferase 1


Mass: 24400.057 Da / Num. of mol.: 1 / Mutation: D46A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: speck
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q94521
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M 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: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→30 Å / Num. obs: 46902 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.04 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.057 / Χ2: 1.07 / Net I/σ(I): 21.82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.53-303.546570.9990.0180.0351.09598.7
2.8-3.533.747110.9990.0180.0351.095100
2.45-2.83.846840.9970.0270.0531.014100
2.23-2.453.747060.9940.0410.081.15599.9
2.07-2.233.747310.9930.0520.1021.05399.9
1.94-2.073.846950.9860.0710.140.984100
1.85-1.943.846950.960.1270.2521.119100
1.77-1.853.846600.3920.1760.3481.06399.9
1.7-1.773.747450.8710.2470.4831.08699.9
1.64-1.73.246180.7840.3370.6341.10698.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
MOLREP6.5phasing
PHENIX1.13_2998refinement
HKL-2000data scaling
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.645→22.744 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.63
RfactorNum. reflection% reflection
Rfree0.2045 1225 4.91 %
Rwork0.1854 --
obs0.1864 24957 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.5172 Å2
Refinement stepCycle: LAST / Resolution: 1.645→22.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 51 238 1986
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
1.645-1.71060.30131210.25422541097
1.7106-1.78850.26231470.21125670100
1.7885-1.88270.25461350.199626180100
1.8827-2.00060.26571330.205126360100
2.0006-2.1550.2251330.182926200100
2.155-2.37160.22071280.19992615099
2.3716-2.71430.20951280.188226730100
2.7143-3.41790.19021590.18326630100
3.4179-22.7440.16761410.16562799099

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