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- PDB-6ag4: Crystal structure of Ard1 N-terminal acetyltransferase H88A/E127A... -

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Basic information

Entry
Database: PDB / ID: 6ag4
TitleCrystal structure of Ard1 N-terminal acetyltransferase H88A/E127A mutant from Sulfolobus solfataricus
ComponentsN-alpha-acetyltransferase
KeywordsTRANSFERASE / Acetyltransferase
Function / homology
Function and homology information


N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / NatA complex / protein N-terminal-serine acetyltransferase activity / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / protein-N-terminal amino-acid 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: 2.256 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)21,1234
Polymers20,1771
Non-polymers9463
Water1,22568
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 area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.335, 53.148, 74.505
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: 20177.338 Da / Num. of mol.: 1 / Mutation: H88A, E127A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: P2 / Gene: SsArd1 / 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


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.75M ammonium sulfate, 0.1M sodium acetate trihydrate, pH 4.2, 0.1M lithium sulfate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 8167 / % possible obs: 98.1 % / Redundancy: 4.9 % / Net I/σ(I): 24.6
Reflection shellResolution: 2.25→2.36 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: 2.256→27.967 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 817 10.01 %
Rwork0.1626 --
obs0.1692 8164 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.256→27.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 57 68 1408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071373
X-RAY DIFFRACTIONf_angle_d1.0221865
X-RAY DIFFRACTIONf_dihedral_angle_d15.824505
X-RAY DIFFRACTIONf_chiral_restr0.041201
X-RAY DIFFRACTIONf_plane_restr0.005228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2556-2.39680.26491240.17341118X-RAY DIFFRACTION91
2.3968-2.58170.30421340.18971196X-RAY DIFFRACTION98
2.5817-2.84130.25241360.1921229X-RAY DIFFRACTION99
2.8413-3.25190.26351380.18221245X-RAY DIFFRACTION100
3.2519-4.0950.20221390.15051248X-RAY DIFFRACTION100
4.095-27.96880.19661460.14421311X-RAY DIFFRACTION99
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)
13.2793-1.4105-2.76595.85650.88856.4215-0.0278-0.80330.8939-0.21650.27270.0356-1.0487-0.7381-0.00150.36450.0733-0.05330.4485-0.0520.348-17.181211.81767.1846
23.93011.5506-1.7119.5754-4.28266.06510.2324-0.40750.18851.1636-0.5604-0.8815-0.35080.68880.27450.34140.0026-0.07730.3491-0.05570.3157-7.18333.858613.6134
31.82990.14930.47472.61920.2043.73430.0466-0.00480.07-0.02370.2218-0.34080.00660.1912-0.25420.27510.0005-0.01420.2615-0.04080.325-8.35671.48264.5234
42.2365-1.5717-1.2073.21071.65664.7531-0.0668-0.0293-0.14530.1892-0.10260.18150.4706-0.24140.0350.2467-0.0669-0.04950.23140.05460.2326-16.9778-5.85720.2713
53.1297-0.3315-2.31523.0577-0.43698.88760.070.32780.3473-0.44290.04190.4489-0.3596-0.3814-0.06880.29540.0417-0.0540.21090.01140.2914-18.95313.0979-2.4836
61.91290.333-1.03211.92060.77032.27650.07350.1608-0.0408-0.0863-0.18220.26180.0185-0.12440.09460.22140.0147-0.00470.2134-0.00450.2405-20.8386-10.78281.9029
73.5544-1.34250.16752.2534-0.51033.1048-0.2747-0.55080.0390.04340.2519-0.03390.2517-0.30810.0770.32390.04020.01190.23940.02460.2878-15.8457-15.31183.8881
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 11:18 )A11 - 18
2X-RAY DIFFRACTION2( CHAIN A AND RESID 19:32 )A19 - 32
3X-RAY DIFFRACTION3( CHAIN A AND RESID 33:73 )A33 - 73
4X-RAY DIFFRACTION4( CHAIN A AND RESID 74:102 )A74 - 102
5X-RAY DIFFRACTION5( CHAIN A AND RESID 103:119 )A103 - 119
6X-RAY DIFFRACTION6( CHAIN A AND RESID 120:150 )A120 - 150
7X-RAY DIFFRACTION7( CHAIN A AND RESID 151:167 )A151 - 167

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