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- PDB-5gii: Crystal Structure of Drosophila melanogaster E47N Dopamine N-Acet... -

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Basic information

Entry
Database: PDB / ID: 5gii
TitleCrystal Structure of Drosophila melanogaster E47N 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 / 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-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: 1.294 Å
AuthorsYang, Y.C. / Wu, C.Y. / Cheng, H.C. / Lyu, P.C.
CitationJournal: To Be Published
Title: Crystal Structure of Drosophila melanogaster E47N 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)25,3583
Polymers24,4271
Non-polymers9312
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.824, 56.279, 84.629
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: 24427.037 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 56-265 / Mutation: E47N
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.: 255 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1.0M NaH2PO4, 1.6M K2HPO4, 0.1M Imidazole, 0.2M NaCl
PH range: 6.5-7.0

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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: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.29→30 Å / Num. obs: 52625 / % possible obs: 99 % / Redundancy: 7.7 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.034 / Net I/av σ(I): 51.011 / Net I/σ(I): 18.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.29-1.347.10.489194.8
1.34-1.397.80.37198.9
1.39-1.457.80.259199.2
1.45-1.537.80.167199.3
1.53-1.637.90.107199.4
1.63-1.757.90.074199.8
1.75-1.937.90.047199.8
1.93-2.217.80.0411100
2.21-2.787.60.0351100
2.78-307.50.02198.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.35 Å28.14 Å
Translation1.35 Å28.14 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: 1.294→28.139 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.9
RfactorNum. reflection% reflection
Rfree0.1865 2628 5 %
Rwork0.1596 --
obs0.1609 52570 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 44.24 Å2 / Biso mean: 19.79 Å2 / Biso min: 8.86 Å2
Refinement stepCycle: final / Resolution: 1.294→28.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 60 255 2002
Biso mean--16.21 29.93 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061789
X-RAY DIFFRACTIONf_angle_d1.2352420
X-RAY DIFFRACTIONf_chiral_restr0.081254
X-RAY DIFFRACTIONf_plane_restr0.006310
X-RAY DIFFRACTIONf_dihedral_angle_d16.385689
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 (%)
1.2937-1.31730.25291300.19212496262695
1.3173-1.34260.20511370.16322583272099
1.3426-1.370.1851380.14762614275299
1.37-1.39980.18881360.14122564270099
1.3998-1.43240.18271360.13642585272199
1.4324-1.46820.18081370.13572596273399
1.4682-1.50790.17881380.1292610274899
1.5079-1.55220.16041380.12112598273699
1.5522-1.60230.15861370.1262614275199
1.6023-1.65960.1691390.125626272766100
1.6596-1.7260.17131370.13526102747100
1.726-1.80460.17371390.13926422781100
1.8046-1.89970.19671390.140326372776100
1.8997-2.01870.18041400.140626562796100
2.0187-2.17450.1821410.145526732814100
2.1745-2.39320.16791390.160526592798100
2.3932-2.73930.21151430.183527142857100
2.7393-3.45020.20041400.180626882828100
3.4502-28.14610.18431440.17662776292097

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