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

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Basic information

Entry
Database: PDB / ID: 7civ
TitleCrystal Structure of Agmatine N-Acetyltransferase mutant S171A in complex with Ac-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
ACETYL COENZYME *A / aralkylamine N-acetyltransferase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.848 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 in complex with Ac-CoA
Authors: Chen, J.J. / Hu, I.C. / Lai, C.H. / Lyu, P.C.
History
DepositionJul 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Agmatine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5932
Polymers23,7831
Non-polymers8101
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-3 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.202, 51.676, 81.928
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-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.97 Å3/Da / Density % sol: 37.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium HEPES (pH7.0), 2.1M ammonium sulfate, soaked in 20mM Ac-CoA for 4 hours

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.848→30 Å / Num. obs: 16586 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.071 / Rrim(I) all: 0.172 / Χ2: 1.032 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.9230.61415720.6840.4090.7421.05898.1
1.92-1.993.60.52416300.7670.3180.6161.04799.5
1.99-2.084.30.41216310.8710.2240.4711.02399.9
2.08-2.194.90.38616400.9220.1930.4321.039100
2.19-2.335.50.36116500.9420.170.41.029100
2.33-2.516.20.36516400.9460.160.41.031100
2.51-2.766.70.33416590.9690.140.3621.044100
2.76-3.166.70.22216750.9760.0930.2411.04599.9
3.16-3.986.40.11317050.9910.0490.1231.02499.9
3.98-305.60.06817840.9960.0310.0750.99999.6

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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: 1.848→22.101 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 1655 10 %
Rwork0.1909 14889 -
obs0.1959 16544 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.54 Å2 / Biso mean: 23.9333 Å2 / Biso min: 11.74 Å2
Refinement stepCycle: final / Resolution: 1.848→22.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 51 111 1826
Biso mean--27.69 28.57 -
Num. residues----215
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.848-1.90230.28941290.2385115394
1.9023-1.96370.24861310.2218118599
1.9637-2.03380.25661350.19961225100
2.0338-2.11520.28051390.19381241100
2.1152-2.21140.26941370.19351230100
2.2114-2.32780.21751380.18941245100
2.3278-2.47350.25171370.19991234100
2.4735-2.66420.29841360.20431228100
2.6642-2.93180.23571410.21571268100
2.9318-3.35470.26331390.19851250100
3.3547-4.22180.20061430.17271281100
4.2218-22.1010.22261500.17131349100

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