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- PDB-7cix: Crystal Structure of Agmatine N-Acetyltransferase mutant S171A in... -

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Basic information

Entry
Database: PDB / ID: 7cix
TitleCrystal Structure of Agmatine N-Acetyltransferase mutant S171A in complex with CoA
ComponentsAgmatine N-acetyltransferase
KeywordsTRANSFERASE / GCN5-related N-acetyltransferase(GNAT) / Arylalkylamine N-acetyltransferase(AANAT)
Function / homology
Function and homology information


aralkylamine N-acetyltransferase activity / aralkylamine N-acetyltransferase / arylamine N-acetyltransferase activity / N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
COENZYME A / aralkylamine N-acetyltransferase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.748 Å
AuthorsChen, J.J. / Hu, I.C. / Wu, C.Y. / Lyu, P.C.
Funding support1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)
CitationJournal: To Be Published
Title: Crystal Structure of Agmatine N-Acetyltransferase mutant S171A in complex with CoA
Authors: Chen, J.J. / Hu, I.C. / Wu, C.Y. / Lyu, P.C.
History
DepositionJul 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Agmatine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5512
Polymers23,7831
Non-polymers7681
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-1 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.199, 51.585, 81.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Agmatine N-acetyltransferase


Mass: 23783.109 Da / Num. of mol.: 1 / Mutation: S171A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: AgmNAT, AANATL8, Dmel\CG15766, CG15766, Dmel_CG15766 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9W469, arylamine N-acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium HEPES (pH7.0), 2.1M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.748→30 Å / Num. obs: 19454 / % possible obs: 99.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Χ2: 1.033 / Net I/σ(I): 25.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.815.20.52918810.8750.2560.5891.00699.9
1.81-1.896.10.36119240.9440.1590.3951.054100
1.89-1.976.40.24219170.9760.1030.2641.059100
1.97-2.076.30.15519250.990.0660.1691.05899.9
2.07-2.26.40.10619290.9940.0450.1151.054100
2.2-2.376.40.07819110.9960.0330.0851.05999.4
2.37-2.616.50.06319530.9980.0270.0691.02199.7
2.61-2.996.80.04419330.9990.0180.0481.0199.8
2.99-3.776.90.0319930.9990.0120.0321.02399.8
3.77-306.30.02820880.9990.0120.0310.98499.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.17 Å25.9 Å
Translation5.17 Å25.9 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.8.3phasing
PHENIX1.16refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k9n

5k9n


Resolution: 1.748→25.899 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2155 1941 10 %
Rwork0.179 17467 -
obs0.1827 19408 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.26 Å2 / Biso mean: 27.4226 Å2 / Biso min: 14.89 Å2
Refinement stepCycle: final / Resolution: 1.748→25.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 48 167 1887
Biso mean--32.41 33.31 -
Num. residues----216
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7482-1.79190.29721330.2247120399
1.7919-1.84040.29341380.21491242100
1.8404-1.89450.3121360.19821219100
1.8945-1.95560.26451350.19931214100
1.9556-2.02550.22981380.21236100
2.0255-2.10660.22741380.1831244100
2.1066-2.20240.24151370.18321242100
2.2024-2.31840.21821380.18161235100
2.3184-2.46360.24061380.1884123499
2.4636-2.65360.22741360.19361233100
2.6536-2.92030.2291410.19181267100
2.9203-3.34220.20991390.18171251100
3.3422-4.20780.19031430.15521293100
4.2078-25.8990.18041510.16621354100

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