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

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Basic information

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


aralkylamine N-acetyltransferase / aralkylamine N-acetyltransferase activity / arylamine N-acetyltransferase activity / N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
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 / N-(4-carbamimidamidobutyl)ethanamide / Agmatine N-acetyltransferase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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 Ac-Agm and CoA
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7233
Polymers23,7831
Non-polymers9402
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-0 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.911, 51.235, 78.459
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
#3: Chemical ChemComp-G0R / N-(4-carbamimidamidobutyl)ethanamide


Mass: 172.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.81 Å3/Da / Density % sol: 32.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium HEPES (pH7.0), 2.0M 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: Oct 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.599→30 Å / Num. obs: 23468 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.031 / Rrim(I) all: 0.079 / Χ2: 1.057 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.664.50.76122830.6180.3870.8581.08698.6
1.66-1.726.20.66723040.8110.2880.7281.07799.6
1.72-1.86.70.49222910.9030.2020.5321.08299.8
1.8-1.96.80.31523260.9560.1290.3411.05299.7
1.9-2.026.60.20623220.9790.0860.2241.06599.8
2.02-2.176.90.12823280.9910.0520.1380.994100
2.17-2.3970.08723650.9960.0350.0941.004100
2.39-2.747.10.06823420.9970.0270.0731.072100
2.74-3.4570.04424120.9990.0180.0470.977100
3.45-306.10.04124950.9980.0180.0451.19898.9

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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: 1.6→25.207 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 2000 8.54 %
Rwork0.1844 21419 -
obs0.1885 23419 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.93 Å2 / Biso mean: 21.359 Å2 / Biso min: 9.83 Å2
Refinement stepCycle: final / Resolution: 1.6→25.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 60 155 1887
Biso mean--20.13 28.29 -
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 (%)
1.6-1.63920.31961370.282147097
1.6392-1.68350.30591380.244148299
1.6835-1.7330.25821420.21711514100
1.733-1.78890.28461430.20421528100
1.7889-1.85280.23431400.1861498100
1.8528-1.9270.24261390.18891496100
1.927-2.01470.2441430.18711532100
2.0147-2.12080.19621430.1711522100
2.1208-2.25360.23011420.17431530100
2.2536-2.42750.22621430.18381536100
2.4275-2.67160.24551450.19821544100
2.6716-3.05760.24481460.18181554100
3.0576-3.850.21171450.16811568100
3.85-25.2070.22571540.1773164599

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