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- PDB-4r3k: Crystal structure of Ard1 N-terminal acetyltransferase from Sulfo... -

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Basic information

Entry
Database: PDB / ID: 4r3k
TitleCrystal structure of Ard1 N-terminal acetyltransferase from Sulfolobus solfataricus bound to CoA
ComponentsUncharacterized N-acetyltransferase SSO0209
KeywordsTRANSFERASE / Protein-substrate complex / GNAT domain / N-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
COENZYME A / N-alpha-acetyltransferase
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.133 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized N-acetyltransferase SSO0209
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3025
Polymers20,3021
Non-polymers1,0004
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.353, 58.224, 85.265
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 Uncharacterized N-acetyltransferase SSO0209 / Ard1


Mass: 20302.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / 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: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 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: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→30 Å / Num. obs: 10196 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 18.876
Reflection shellHighest resolution: 2.13 Å

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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: 2.133→22.151 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 1018 9.99 %RANDOM
Rwork0.172 ---
obs0.1765 10191 98.98 %-
all-10191 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.133→22.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 59 39 1389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071379
X-RAY DIFFRACTIONf_angle_d1.1291873
X-RAY DIFFRACTIONf_dihedral_angle_d18.173521
X-RAY DIFFRACTIONf_chiral_restr0.043199
X-RAY DIFFRACTIONf_plane_restr0.005229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1332-2.24550.24541360.21521236123695
2.2455-2.38610.29521430.198812831283100
2.3861-2.57010.27851430.20112951295100
2.5701-2.82820.20161460.183713011301100
2.8282-3.23640.2631480.182713311331100
3.2364-4.07340.181470.157113261326100
4.0734-22.15210.19341550.15571401140199
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)
12.9556-0.8106-0.98727.22940.02395.23570.2423-0.65580.25451.3171-0.2087-0.4937-0.47980.3905-0.14220.4531-0.0305-0.02450.2924-0.03190.34624.37969.86525.3287
23.40022.12280.11426.1394-0.2145.11890.1402-0.02490.39170.3028-0.0017-0.0323-0.0910.1551-0.05970.29110.06030.03210.1796-0.04510.28670.732213.405919.6922
36.8929-2.01745.31553.2458-2.7044.4708-0.2550.34740.62130.4155-0.1956-0.083-0.61210.33090.56840.249-0.0180.0280.22480.00340.3297-2.44829.682212.7142
44.94891.05263.70671.2761-1.35329.88021.00623.0523-0.4457-2.4437-0.34560.97091.6884-0.3621-0.38380.87370.2172-0.21570.8952-0.05460.5879-7.82384.1859-6.2301
56.5672-1.61034.46415.2297-1.35827.4844-0.0663-0.19320.32270.1811-0.0668-0.50450.21690.17390.11870.16280.01720.08540.19550.05530.27044.58364.053314.8603
62.4252-2.77641.85033.4024-1.51194.91640.2818-0.011-0.4322-0.2571-0.08580.47880.6985-0.16550.03990.3389-0.03080.02610.16970.01540.2858-3.7339-0.371215.6634
72.1869-0.7285-2.32933.9075-0.44374.5929-0.09580.27580.3948-0.2966-0.00990.21530.0862-0.1187-0.05240.2932-0.0016-0.00280.2141-0.02270.2448-0.50525.39476.6778
87.82812.8249-1.46895.4311-1.6256.4616-0.6482-0.1396-1.2259-0.76090.3509-0.67650.57330.21640.23790.4725-0.00310.07270.27750.00730.36056.7728-0.99774.2365
94.81831.7159-1.09314.2038-0.50124.5064-0.7620.0452-0.3949-1.38540.5309-0.4262-0.02140.49520.03540.4707-0.04430.07280.3198-0.02190.27637.10177.61131.4773
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 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 74 )
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 82 )
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 102 )
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 117 )
7X-RAY DIFFRACTION7chain 'A' and (resid 118 through 132 )
8X-RAY DIFFRACTION8chain 'A' and (resid 133 through 150 )
9X-RAY DIFFRACTION9chain 'A' and (resid 151 through 167 )

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