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- PDB-5k9n: Structural and Mechanistic Analysis of Drosophila melanogaster Po... -

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Basic information

Entry
Database: PDB / ID: 5k9n
TitleStructural and Mechanistic Analysis of Drosophila melanogaster Polyamine N acetyltransferase, an enzyme that Catalyzes the Formation of N acetylagmatine
ComponentsPolyamine N acetyltransferase
KeywordsTRANSFERASE / Polyamine N acetyltransferase / agmatine / N acetylagmatine / Drosophila melanogaster / enzyme mechanism / acetyl-CoA / and protein crystallography
Function / homology
Function and homology information


arylamine N-acetyltransferase / aralkylamine N-acetyltransferase activity / arylamine N-acetyltransferase activity / N-acetyltransferase activity
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
Agmatine N-acetyltransferase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsDempsey, D.R. / Nichols, D.A. / Battistini, M.R. / Pemberton, O. / Ospina, S.R. / Zhang, X. / Carpenter, A.-M. / Chen, Y. / Merkler, D.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R03 DA034323 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15-GM107864 United States
CitationJournal: Sci Rep / Year: 2017
Title: Structural and Mechanistic Analysis of Drosophila melanogaster Agmatine N-Acetyltransferase, an Enzyme that Catalyzes the Formation of N-Acetylagmatine.
Authors: Dempsey, D.R. / Nichols, D.A. / Battistini, M.R. / Pemberton, O. / Ospina, S.R. / Zhang, X. / Carpenter, A.M. / O'Flynn, B.G. / Leahy, J.W. / Kanwar, A. / Lewandowski, E.M. / Chen, Y. / Merkler, D.J.
History
DepositionJun 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 1, 2017Group: 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 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 28, 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: Polyamine N acetyltransferase
B: Polyamine N acetyltransferase


Theoretical massNumber of molelcules
Total (without water)47,5982
Polymers47,5982
Non-polymers00
Water64936
1
A: Polyamine N acetyltransferase


Theoretical massNumber of molelcules
Total (without water)23,7991
Polymers23,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polyamine N acetyltransferase


Theoretical massNumber of molelcules
Total (without water)23,7991
Polymers23,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.110, 72.350, 59.520
Angle α, β, γ (deg.)90.00, 109.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyamine N acetyltransferase


Mass: 23799.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG15766, Dmel_CG15766 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9W469, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris , 200 mM sodium acetate, 30% PEG 4000 / PH range: 8

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→56.09 Å / Num. obs: 18703 / % possible obs: 100 % / Redundancy: 3.6 % / Net I/σ(I): 6.3

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Processing

Software
NameVersionClassification
PHENIX1.6.1_357refinement
iMOSFLMdata reduction
RefinementResolution: 2.3→44.313 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 28.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2878 1443 8.14 %
Rwork0.2078 --
obs0.2143 17718 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.99 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3931 Å20 Å22.6132 Å2
2--4.6861 Å20 Å2
3----9.0792 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 0 36 3290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083332
X-RAY DIFFRACTIONf_angle_d1.1814541
X-RAY DIFFRACTIONf_dihedral_angle_d16.2461223
X-RAY DIFFRACTIONf_chiral_restr0.077513
X-RAY DIFFRACTIONf_plane_restr0.006602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.38230.34791290.24381481X-RAY DIFFRACTION87
2.3823-2.47760.341360.2271550X-RAY DIFFRACTION90
2.4776-2.59040.27961360.22111569X-RAY DIFFRACTION93
2.5904-2.72690.30191420.22261572X-RAY DIFFRACTION94
2.7269-2.89780.33671420.23181633X-RAY DIFFRACTION95
2.8978-3.12140.3151460.23291630X-RAY DIFFRACTION96
3.1214-3.43550.30141500.21831689X-RAY DIFFRACTION99
3.4355-3.93230.27791510.19181685X-RAY DIFFRACTION99
3.9323-4.95320.24431550.16591728X-RAY DIFFRACTION99
4.9532-44.32090.22561560.18321738X-RAY DIFFRACTION99

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