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- PDB-4fd7: Crystal structure of insect putative arylalkylamine N-Acetyltrans... -

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Basic information

Entry
Database: PDB / ID: 4fd7
TitleCrystal structure of insect putative arylalkylamine N-Acetyltransferase 7 from the yellow fever mosquito Aedes aegypt
Componentsputative arylalkylamine N-Acetyltransferase 7
KeywordsTRANSFERASE / Gnat / CoA binding
Function / homology
Function and homology information


N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHan, Q. / Robinson, R. / Li, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Evolution of insect arylalkylamine N-acetyltransferases: structural evidence from the yellow fever mosquito, Aedes aegypti.
Authors: Han, Q. / Robinson, H. / Ding, H. / Christensen, B.M. / Li, J.
History
DepositionMay 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Sep 13, 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: putative arylalkylamine N-Acetyltransferase 7
B: putative arylalkylamine N-Acetyltransferase 7
C: putative arylalkylamine N-Acetyltransferase 7
D: putative arylalkylamine N-Acetyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,78426
Polymers109,4094
Non-polymers2,37522
Water18,0871004
1
A: putative arylalkylamine N-Acetyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0497
Polymers27,3521
Non-polymers6976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: putative arylalkylamine N-Acetyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1458
Polymers27,3521
Non-polymers7937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: putative arylalkylamine N-Acetyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9537
Polymers27,3521
Non-polymers6016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: putative arylalkylamine N-Acetyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6374
Polymers27,3521
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.671, 89.281, 92.442
Angle α, β, γ (deg.)90.00, 96.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
putative arylalkylamine N-Acetyltransferase 7


Mass: 27352.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Strain: Liverpool / Gene: AAEL012870, AaeL_AAEL012870 / Plasmid: ptyb / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: Q16KU7, aralkylamine N-acetyltransferase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1004 / 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: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.5 M sodium chloride, 25.5% polyethylene glycol 8000, 15% glycerol and 0.1 M sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.54 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 94402 / Redundancy: 7 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 11.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FD5

4fd5


Resolution: 1.8→40 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.882 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2704 4727 5 %RANDOM
Rwork0.22571 ---
obs0.22796 89479 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.768 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7648 0 49 1004 8701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197843
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.94210604
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6585944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30823.235408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.098151320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0011576
X-RAY DIFFRACTIONr_chiral_restr0.0810.21139
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216056
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 327 -
Rwork0.257 6582 -
obs--99.61 %

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