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- PDB-4r3l: Crystal structure of Ard1 N-terminal acetyltransferase from Sulfo... -

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Basic information

Entry
Database: PDB / ID: 4r3l
TitleCrystal structure of Ard1 N-terminal acetyltransferase from Sulfolobus solfataricus bound to substrate peptide fragment and CoA
Components
  • N-terminal 6-mer peptide from Alba
  • Uncharacterized N-acetyltransferase SSO0209
KeywordsTRANSFERASE/TRANSFERASE SUBSTRATE / Protein-substrate complex / GNAT domain / N-acetyltransferase / TRANSFERASE-TRANSFERASE SUBSTRATE complex
Function / homology
Function and homology information


N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / NatA complex / peptide alpha-N-acetyltransferase activity / nuclease activity / chromosome condensation / chromosome / double-stranded DNA binding / Hydrolases; Acting on ester bonds / RNA binding ...N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / NatA complex / peptide alpha-N-acetyltransferase activity / nuclease activity / chromosome condensation / chromosome / double-stranded DNA binding / Hydrolases; Acting on ester bonds / RNA binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
N-acetyltransferase RimI/Ard1 / DNA/RNA-binding protein Alba / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / N-acetyltransferase Ard1-like / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain ...N-acetyltransferase RimI/Ard1 / DNA/RNA-binding protein Alba / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / N-acetyltransferase Ard1-like / 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
COENZYME A / DNA/RNA-binding protein Alba 1 / N-alpha-acetyltransferase
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
Sulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.839 Å
AuthorsChang, Y.Y. / Hsu, C.H.
CitationJournal: Sci Rep / Year: 2015
Title: Structural Basis for Substrate-specific Acetylation of N alpha-acetyltransferase Ard1 from Sulfolobus solfataricus
Authors: Chang, Y.Y. / Hsu, C.H.
History
DepositionAug 16, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized N-acetyltransferase SSO0209
B: N-terminal 6-mer peptide from Alba
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6193
Polymers20,8512
Non-polymers7681
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-2 kcal/mol
Surface area8100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.185, 58.004, 84.109
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized N-acetyltransferase SSO0209


Mass: 20302.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: P2 / Gene: SSO0209 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q980R9, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide N-terminal 6-mer peptide from Alba


Mass: 548.545 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: the peptide sequence derived from Alba protein in Sulfolobus solfataricus
Source: (synth.) Sulfolobus solfataricus (archaea) / References: UniProt: P60849*PLUS
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 12.5% PEG 4000, 0.1M sodium acetate trihydrate pH 4.2, 0.1M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 28, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.839→30 Å / Num. obs: 15532 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X7B

2x7b


Resolution: 1.839→23.875 Å / σ(F): 0 / σ(I): -3 / Stereochemistry target values: ML
RfactorNum. reflectionSelection details
Rfree0.2454 1554 RANDOM
Rwork0.1903 --
obs0.1957 15532 -
all-15532 -
Refinement stepCycle: LAST / Resolution: 1.839→23.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 48 85 1436
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.09
X-RAY DIFFRACTIONf_dihedral_angle_d16.956
X-RAY DIFFRACTIONf_chiral_restr0.043
X-RAY DIFFRACTIONf_plane_restr0.005
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
1.8394-1.89880.28441380.24051240100
1.8988-1.96660.25031390.20651255100
1.9666-2.04530.23521400.18731254100
2.0453-2.13830.23651380.18931241100
2.1383-2.2510.23731390.18991260100
2.251-2.39190.26791400.19291257100
2.3919-2.57640.25561410.20121263100
2.5764-2.83530.25341410.19621271100
2.8353-3.24470.25331430.20051290100
3.2447-4.08460.24381430.17631285100
4.0846-23.87710.23231520.1848136599

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