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- PDB-5gih: Crystal Structure of Drosophila melanogaster E47D Dopamine N-Acet... -

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Basic information

Entry
Database: PDB / ID: 5gih
TitleCrystal Structure of Drosophila melanogaster E47D Dopamine N-Acetyltransferase in Ternary Complex with CoA and Acetyl-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
N-(2-phenylethyl)acetamide / COENZYME A / Arylalkylamine N-acetyltransferase 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.392 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 Ternary Complex with CoA and Acetyl-phenylethylamine
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

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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)25,3593
Polymers24,4281
Non-polymers9312
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.554, 56.186, 84.298
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: 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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-54W / N-(2-phenylethyl)acetamide


Mass: 163.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.39→30 Å / Num. obs: 41932 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 16.14 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.029 / Rrim(I) all: 0.074 / Χ2: 1.061 / Net I/av σ(I): 23.931 / Net I/σ(I): 12.3 / Num. measured all: 270484
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.39-1.445.60.77940680.6870.350.8580.95498.3
1.44-1.56.40.59741560.8310.2520.651.085100
1.5-1.576.70.40141270.9210.1660.4351.08999.9
1.57-1.656.70.28941830.9550.1190.3131.09399.9
1.65-1.756.80.20141780.9810.0830.2181.084100
1.75-1.896.80.13241670.9910.0550.1431.09299.9
1.89-2.086.70.08242160.9950.0350.0891.05399.9
2.08-2.386.50.06641980.9960.0290.0721.06599.8
2.38-2.996.20.06342720.9960.0280.0690.99399.7
2.99-306.20.04243670.9980.0180.0461.07397.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.39 Å26.66 Å
Translation1.39 Å26.66 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: 1.392→26.661 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.96
RfactorNum. reflection% reflection
Rfree0.1944 2093 5 %
Rwork0.156 --
obs0.1579 41870 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 49.16 Å2 / Biso mean: 20.46 Å2 / Biso min: 9.81 Å2
Refinement stepCycle: final / Resolution: 1.392→26.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 60 229 1976
Biso mean--15.06 30.68 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051789
X-RAY DIFFRACTIONf_angle_d1.1832420
X-RAY DIFFRACTIONf_chiral_restr0.078254
X-RAY DIFFRACTIONf_plane_restr0.006310
X-RAY DIFFRACTIONf_dihedral_angle_d16.271689
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3924-1.42480.23191310.1932493262495
1.4248-1.46040.24341380.170726242762100
1.4604-1.49990.20771400.156926412781100
1.4999-1.5440.21421370.139226172754100
1.544-1.59380.17321390.129826232762100
1.5938-1.65080.18181400.126526592799100
1.6508-1.71690.16371380.123126252763100
1.7169-1.7950.20631400.126926592799100
1.795-1.88960.19881400.132626502790100
1.8896-2.0080.19231400.132426602800100
2.008-2.1630.1751420.135126922834100
2.163-2.38050.18791400.150626492789100
2.3805-2.72470.2351410.171127122853100
2.7247-3.43160.20631430.17462688283199
3.4316-26.66610.17691440.17152785292997

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