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- PDB-3v8i: Crystal Structure of a Drosophila melanogaster Dopamine N-Acetylt... -

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Basic information

Entry
Database: PDB / ID: 3v8i
TitleCrystal Structure of a Drosophila melanogaster Dopamine N-Acetyltransferase
ComponentsDopamine N acetyltransferase, isoform A
KeywordsTRANSFERASE / N-acetyltransferase
Function / homology
Function and homology information


chitin-based cuticle sclerotization / serotonin catabolic process / octopamine catabolic process / aralkylamine N-acetyltransferase / aralkylamine N-acetyltransferase activity / arylamine N-acetyltransferase activity / melatonin biosynthetic process / regulation of circadian sleep/wake cycle, sleep / catecholamine metabolic process / dopamine catabolic process ...chitin-based cuticle sclerotization / serotonin catabolic process / octopamine catabolic process / aralkylamine N-acetyltransferase / aralkylamine N-acetyltransferase activity / arylamine N-acetyltransferase activity / melatonin biosynthetic process / regulation of circadian sleep/wake cycle, sleep / catecholamine metabolic process / dopamine catabolic process / sleep / N-acetyltransferase activity / nucleus / cytoplasm
Similarity search - Function
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
Arylalkylamine N-acetyltransferase 1 / Arylalkylamine N-acetyltransferase 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.802 Å
AuthorsCheng, K.-C. / Lyu, P.-C.
CitationJournal: To be Published
Title: Crystal Structure of a Drosophila melanogaster Dopamine N-Acetyltransferase
Authors: Cheng, K.-C. / Lyu, P.-C.
History
DepositionDec 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dopamine N acetyltransferase, isoform A
B: Dopamine N acetyltransferase, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5384
Polymers48,0612
Non-polymers4772
Water11,746652
1
A: Dopamine N acetyltransferase, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2692
Polymers24,0311
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dopamine N acetyltransferase, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2692
Polymers24,0311
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.838, 52.511, 67.594
Angle α, β, γ (deg.)74.05, 90.05, 73.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Dopamine N acetyltransferase, isoform A / GH12636p


Mass: 24030.592 Da / Num. of mol.: 2 / Fragment: UNP residues 21-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG3318, DAT, Dmel_CG3318 / Plasmid: pGEX-6p-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8MKK2, UniProt: Q94521*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, arylamine N-acetyltransferase, aralkylamine N-acetyltransferase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.7 Å3/Da / Density % sol: 54.37 % / Mosaicity: 1.012 °
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.0M NaH2PO4/1.6M K2HPO4, 0.1M HEPES, 0.2M NaCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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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: Mar 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 44004 / % possible obs: 95.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.065 / Χ2: 1.061 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.864.20.31643511.093194.6
1.86-1.944.20.2343751.094194.7
1.94-2.034.20.16943591.092194.7
2.03-2.134.10.12144011.063194.8
2.13-2.274.10.10144321.023195.9
2.27-2.444.10.08244381.075195.7
2.44-2.694.10.07344311.059195.7
2.69-3.084.10.05744371.045195.9
3.08-3.883.80.04442901.024193.1
3.88-303.80.03944901.038196.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.58 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.35 Å
Translation2.5 Å26.35 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHENIX1.6.1_357refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TE4

3te4


Resolution: 1.802→26.352 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.23 / σ(F): 0.04 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 4273 10.03 %
Rwork0.1796 --
obs0.184 42622 91.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.375 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso max: 126.52 Å2 / Biso mean: 24.7988 Å2 / Biso min: 5.79 Å2
Baniso -1Baniso -2Baniso -3
1--5.7151 Å2-0.2638 Å20.0538 Å2
2--7.3136 Å2-0.5137 Å2
3----1.5985 Å2
Refinement stepCycle: LAST / Resolution: 1.802→26.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 30 652 4056
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_refined_d0.006
X-RAY DIFFRACTIONf_angle_refined_deg0.997
LS refinement shellResolution: 1.8→1.89 Å
RfactorNum. reflection
Rfree0.2642 406
Rwork0.1976 -
obs-3447
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4394-0.19870.45411.14860.10460.5940.0381-0.22390.00010.35010.0308-0.09030.0165-0.0979-0.0730.159-0.0101-0.00470.1392-0.00490.107424.7245-12.1576-23.689
20.50090.2726-0.17740.2224-0.16020.11410.0076-0.2884-0.37610.0682-0.0492-0.06460.01020.09180.05020.1415-0.0099-0.01720.13410.06030.183616.561-24.7083-25.986
30.6559-0.118-0.19720.73270.94331.19730.0461-0.01890.0925-0.17010.0832-0.172-0.24850.008-0.07770.07830.0171-0.00720.0823-0.01340.07924.4857-9.5826-31.9852
40.8902-0.08480.19330.98690.35590.22040.02840.312-0.1008-0.4267-0.1367-0.0680.22290.16940.10930.21580.04830.02610.14610.01810.114814.3156-28.0957-39.3042
50.8230.07160.04690.51780.16850.1085-0.05180.12440.0243-0.06130.06270.01680.06420.0337-0.02140.0696-0.00470.01140.0950.00360.037116.1382-7.3477-37.2989
60.398-0.2384-0.09450.3130.06620.1771-0.00290.07280.0665-0.0561-0.0250.10610.0249-0.09160.00110.0901-0.0045-0.00240.078-0.00940.07633.5206-15.676-33.2497
70.3066-0.1256-0.21120.6116-0.14010.78330.1312-0.00320.0030.14670.00920.1204-0.172-0.2393-0.12530.12790.01440.02310.09770.00770.0671-7.2317-8.5524-60.0156
80.593-0.1843-0.07250.1813-0.12390.2812-0.0729-0.13660.18490.08690.0991-0.1378-0.04930.008-0.0160.2071-0.00180.01650.1595-0.0370.18790.83010.7043-68.9976
90.51160.13820.12730.2550.1520.87190.0301-0.1493-0.0170.0180.0766-0.04810.0797-0.1735-0.06820.07010.0237-0.00130.11670.00950.0606-6.981-15.2658-65.5616
100.8052-0.0761-0.16150.753-0.78520.9340.03280.18620.1522-0.3846-0.0392-0.11220.1798-0.08670.0050.1880.0086-0.01350.1134-0.00750.11543.0214-3.9839-81.7936
110.66440.0891-0.01330.238-0.12980.9044-0.02110.0348-0.0838-0.0223-0.0199-0.0214-0.0212-0.10130.03040.06550.0008-0.00260.0754-0.00780.06544.1569-19.0802-68.0487
120.4916-0.2752-0.19010.18380.11850.48140.05480.0177-0.01540.0062-0.0901-0.1299-0.08470.04230.02510.1193-0.02240.00210.10110.02480.093715.0973-6.7988-72.8515
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 21:46)A21 - 46
2X-RAY DIFFRACTION2(chain A and resid 47:67)A47 - 67
3X-RAY DIFFRACTION3(chain A and resid 68:96)A68 - 96
4X-RAY DIFFRACTION4(chain A and resid 97:125)A97 - 125
5X-RAY DIFFRACTION5(chain A and resid 126:182)A126 - 182
6X-RAY DIFFRACTION6(chain A and resid 183:230)A183 - 230
7X-RAY DIFFRACTION7(chain B and resid 21:46)B21 - 46
8X-RAY DIFFRACTION8(chain B and resid 47:67)B47 - 67
9X-RAY DIFFRACTION9(chain B and resid 68:96)B68 - 96
10X-RAY DIFFRACTION10(chain B and resid 97:125)B97 - 125
11X-RAY DIFFRACTION11(chain B and resid 126:201)B126 - 201
12X-RAY DIFFRACTION12(chain B and resid 202:230)B202 - 230

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