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- PDB-7ciu: Crystal Structure of Agmatine N-Acetyltransferase mutant S171A ap... -

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Basic information

Entry
Database: PDB / ID: 7ciu
TitleCrystal Structure of Agmatine N-Acetyltransferase mutant S171A apo form
ComponentsAgmatine N-acetyltransferase
KeywordsTRANSFERASE / GCN5-related N-acetyltransferase(GNAT) / Arylalkylamine N-acetyltransferase(AANAT)
Function / homologyarylamine N-acetyltransferase / aralkylamine N-acetyltransferase activity / arylamine N-acetyltransferase activity / N-acetyltransferase activity / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Agmatine N-acetyltransferase
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.825 Å
AuthorsChen, J.J. / Hu, I.C. / Lai, C.H. / Lyu, P.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: To Be Published
Title: Crystal Structure of Agmatine N-Acetyltransferase mutant S171A
Authors: Chen, J.J. / Hu, I.C. / Lai, C.H. / 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
B: Agmatine N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)47,5662
Polymers47,5662
Non-polymers00
Water5,044280
1
A: Agmatine N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)23,7831
Polymers23,7831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Agmatine N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)23,7831
Polymers23,7831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.201, 59.905, 64.850
Angle α, β, γ (deg.)90.000, 93.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Agmatine N-acetyltransferase


Mass: 23783.109 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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 Å3/Da / Density % sol: 38.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium HEPES (pH7.0), 1.6M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 15, 2019
Diffraction measurementDetails: 1.00 degrees, 0.1 sec, detector distance 230.00 mm / Method: \w scans
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionAv R equivalents: 0.118 / Number: 189658
ReflectionResolution: 1.82→30 Å / Num. obs: 33244 / % possible obs: 99 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.052 / Rrim(I) all: 0.13 / Χ2: 1 / Net I/σ(I): 9.6 / Num. measured all: 189658
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.82-1.893.60.43132970.8730.2620.5050.97198.4
1.89-1.963.70.31532910.8950.1890.3680.99698.7
1.96-2.054.30.23533030.9690.1220.2660.9998.9
2.05-2.165.90.25132920.9750.110.2741.00399.2
2.16-2.296.30.29232980.9560.1260.3190.98998.6
2.29-2.477.20.20133470.9860.0810.2170.98299.6
2.47-2.727.40.14933420.990.0590.161.01299.7
2.72-3.117.20.11433550.9930.0460.1231.00999.9
3.11-3.925.90.0832720.9940.0350.0871.01897.1
3.92-305.50.05134470.9980.0240.0561.01199.8
Cell measurementReflection used: 189658

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5k9n


Resolution: 1.825→25.188 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2702 2005 6.05 %
Rwork0.2121 31157 -
obs0.2155 33162 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.93 Å2 / Biso mean: 19.93 Å2 / Biso min: 4.18 Å2
Refinement stepCycle: final / Resolution: 1.825→25.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 0 280 3495
Biso mean---24.86 -
Num. residues----415
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8253-1.8710.31331400.2423216796
1.871-1.92150.4191340.3131219399
1.9215-1.97810.36231420.2714223699
1.9781-2.04190.27941430.2106220899
2.0419-2.11480.24931480.1957219699
2.1148-2.19940.28831440.2116226199
2.1994-2.29950.35591400.3023215397
2.2995-2.42060.32051510.22352228100
2.4206-2.57210.28061400.20692274100
2.5721-2.77050.26521430.20772233100
2.7705-3.04890.25661450.20922255100
3.0489-3.48910.22521390.19172275100
3.4891-4.39210.23041430.1796217696
4.3921-25.1880.22891530.1892230299

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