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- PDB-4fd4: Crystal structure of mosquito arylalkylamine N-Acetyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 4fd4
TitleCrystal structure of mosquito arylalkylamine N-Acetyltransferase like 5b
Componentsarylalkylamine N-Acetyltransferase like 5b
KeywordsTRANSFERASE / GNAT
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
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. / 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: arylalkylamine N-Acetyltransferase like 5b
B: arylalkylamine N-Acetyltransferase like 5b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9988
Polymers48,4462
Non-polymers5536
Water3,801211
1
A: arylalkylamine N-Acetyltransferase like 5b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4994
Polymers24,2231
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: arylalkylamine N-Acetyltransferase like 5b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4994
Polymers24,2231
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.168, 72.753, 149.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A5 - 217
2116B5 - 217

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Components

#1: Protein arylalkylamine N-Acetyltransferase like 5b


Mass: 24222.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Strain: Liverpool / Gene: AAEL004827, AaeL_AAEL004827 / Plasmid: PTYB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0IFG2, aralkylamine N-acetyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25.5% polyethylene glycol 4000, and 17% glycerol, 0.1 m sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.95→41.18 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 21
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: aaNAT2 from Aedes aegypti

Resolution: 1.95→41.18 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25179 1576 5.1 %RANDOM
Rwork0.20825 ---
obs0.21043 29478 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.376 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 36 211 3579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223420
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9884604
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0375422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75924.11146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12515628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9681520
X-RAY DIFFRACTIONr_chiral_restr0.0820.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212492
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_it3.1151.52100
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.06623382
X-RAY DIFFRACTIONr_scbond_it4.14131320
X-RAY DIFFRACTIONr_scangle_it5.8124.51222
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1666 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.655
Bloose thermal3.6910
LS refinement shellResolution: 1.946→1.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 121 -
Rwork0.254 1873 -
obs--87.34 %

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