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- PDB-5yag: Crystal structure of mosquito arylalkylamine N-Acetyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 5yag
TitleCrystal structure of mosquito arylalkylamine N-Acetyltransferase like 5b/spermine N-Acetyltransferase
ComponentsAAEL004827-PA
KeywordsTRANSFERASE / Transferase Complex N-acetyltransferase Spermine
Function / homology
Function and homology information


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
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHan, Q. / Guan, H. / Robinson, H. / Li, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31472186 China
CitationJournal: PLoS ONE / Year: 2018
Title: Identification of aaNAT5b as a spermine N-acetyltransferase in the mosquito, Aedes aegypti.
Authors: Guan, H. / Wang, M. / Liao, C. / Liang, J. / Mehere, P. / Tian, M. / Liu, H. / Robinson, H. / Li, J. / Han, Q.
History
DepositionAug 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / 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 / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AAEL004827-PA
B: AAEL004827-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0909
Polymers48,4462
Non-polymers6457
Water3,387188
1
A: AAEL004827-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5915
Polymers24,2231
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AAEL004827-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4994
Polymers24,2231
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.258, 72.887, 149.688
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 AAEL004827-PA / spermine N-acetyltransferase


Mass: 24222.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: 5565529, AAEL004827 / Plasmid: PTYB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0IFG2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25.5% polyethylene glycol 4000, 17% glycerol, 0.1 m sodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2013 / Details: 315r
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.948→41.173 Å / Num. obs: 31563 / % possible obs: 99.8 % / Redundancy: 11.7 % / Net I/σ(I): 21
Reflection shellResolution: 1.95→2.02 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FD4

4fd4


Resolution: 1.95→41.17 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.912 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1582 5.1 %RANDOM
Rwork0.2 ---
obs0.203 29716 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.02 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 42 188 3607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193477
X-RAY DIFFRACTIONr_bond_other_d0.0010.023367
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.9894685
X-RAY DIFFRACTIONr_angle_other_deg0.6563.0017805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4665432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25724.189148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62915638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5831520
X-RAY DIFFRACTIONr_chiral_restr0.0640.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023787
X-RAY DIFFRACTIONr_gen_planes_other00.02673
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5583.6181722
X-RAY DIFFRACTIONr_mcbond_other3.5553.6171721
X-RAY DIFFRACTIONr_mcangle_it4.7895.4072150
X-RAY DIFFRACTIONr_mcangle_other4.7895.4082151
X-RAY DIFFRACTIONr_scbond_it4.2854.1371755
X-RAY DIFFRACTIONr_scbond_other4.2834.1371755
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3896.0022534
X-RAY DIFFRACTIONr_long_range_B_refined8.69744.0983944
X-RAY DIFFRACTIONr_long_range_B_other8.743.9433908
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 105 -
Rwork0.263 2097 -
obs--96.33 %

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