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- PDB-6ag5: Crystal structure of Ard1 N-terminal acetyltransferase E88H/H127E... -

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Basic information

Entry
Database: PDB / ID: 6ag5
TitleCrystal structure of Ard1 N-terminal acetyltransferase E88H/H127E mutant from Sulfolobus solfataricus
ComponentsN-alpha-acetyltransferase
KeywordsTRANSFERASE / Acetyltransferase
Function / homology
Function and homology information


N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / peptide alpha-N-acetyltransferase activity / metal ion binding
Similarity search - Function
N-acetyltransferase RimI/Ard1 / 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
ACETYL COENZYME *A / N-alpha-acetyltransferase
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsChang, Y.Y. / Hsu, C.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)103-2113-M-002 -009 -MY2 Taiwan
Citation
Journal: Chem.Commun.(Camb.) / Year: 2020
Title: Adaptation of thermophilic acetyltransferase to a water-mediated catalytic mechanism.
Authors: Chang, Y.Y. / Hagawa, S. / Hsu, C.H.
#1: Journal: SCI REP / Year: 2015
Title: Structural Basis for Substrate-specific Acetylation of Nalpha-acetyltransferase Ard1 from Sulfolobus solfataricus
Authors: Chang, Y.Y. / Hsu, C.H.
History
DepositionAug 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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: N-alpha-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3623
Polymers20,5131
Non-polymers8502
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-17 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.217, 52.926, 73.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein N-alpha-acetyltransferase / NAT / Amino-terminal acetyltransferase / N-terminal acetyltransferase


Mass: 20512.717 Da / Num. of mol.: 1 / Mutation: H88E, E127H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: P2 / Gene: AsArd1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q980R9, N-terminal amino-acid Nalpha-acetyltransferase NatA, N-terminal methionine Nalpha-acetyltransferase NatE
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.1 Å3/Da / Density % sol: 37.12 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.32→30 Å / Num. obs: 7313 / % possible obs: 99.4 % / Redundancy: 6.3 % / Net I/σ(I): 10.69
Reflection shellResolution: 2.3→2.32 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R3K

4r3k


Resolution: 2.32→21.314 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 732 10.01 %
Rwork0.1601 --
obs0.1691 7310 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→21.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 52 100 1444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081374
X-RAY DIFFRACTIONf_angle_d1.1941865
X-RAY DIFFRACTIONf_dihedral_angle_d14.694509
X-RAY DIFFRACTIONf_chiral_restr0.045200
X-RAY DIFFRACTIONf_plane_restr0.005229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3205-2.49940.32221380.20841245X-RAY DIFFRACTION97
2.4994-2.75050.29741450.19361304X-RAY DIFFRACTION100
2.7505-3.14740.25631450.17861310X-RAY DIFFRACTION100
3.1474-3.96120.23891470.1411318X-RAY DIFFRACTION100
3.9612-21.31450.2091570.13651401X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8280.63410.76482.7152-0.10832.50410.03930.1789-0.5806-0.2259-0.0195-0.32540.17620.0175-0.03110.19830.00430.02720.1425-0.04090.1966-10.3257-7.0038-10.56
22-0.6339-0.01641.42490.38663.05980.04490.00770.090.04210.0185-0.1473-0.03050.1771-0.05820.1307-0.01090.01210.12170.00220.159-8.1408-1.7267-4.0923
32.29691.07441.59512.58681.54324.52470.05310.1110.0633-0.2371-0.036-0.0435-0.4-0.04750.02860.12720.05120.03050.13160.06420.1035-16.6056.0028-0.1268
40.3297-0.60530.47261.595-0.92341.21480.055-0.0741-0.07950.02690.03290.11670.05750.0095-0.10310.1171-0.01110.01510.15810.01710.1535-19.77336.1473-0.3566
53.02650.7162-0.92291.6669-0.8193.5677-0.20490.5266-0.05560.0730.14040.11370.11590.19620.02990.1106-0.0375-0.06580.13860.03850.1713-15.383415.2556-3.9874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 73 )
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 102 )
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 167 )

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