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- PDB-4kvx: Crystal structure of Naa10 (Ard1) bound to AcCoA -

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Basic information

Entry
Database: PDB / ID: 4kvx
TitleCrystal structure of Naa10 (Ard1) bound to AcCoA
ComponentsN-terminal acetyltransferase A complex catalytic subunit ard1
KeywordsTRANSFERASE / acetyltransferase
Function / homology
Function and homology information


peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / protein maturation / nucleus / cytosol
Similarity search - Function
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-terminal acetyltransferase A complex catalytic subunit ard1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLiszczak, G.P. / Marmorstein, R.Q.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Molecular basis for N-terminal acetylation by the heterodimeric NatA complex.
Authors: Liszczak, G. / Goldberg, J.M. / Foyn, H. / Petersson, E.J. / Arnesen, T. / Marmorstein, R.
History
DepositionMay 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Sep 20, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-terminal acetyltransferase A complex catalytic subunit ard1
B: N-terminal acetyltransferase A complex catalytic subunit ard1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5254
Polymers36,9062
Non-polymers1,6192
Water4,720262
1
A: N-terminal acetyltransferase A complex catalytic subunit ard1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2622
Polymers18,4531
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-terminal acetyltransferase A complex catalytic subunit ard1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2622
Polymers18,4531
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.974, 64.833, 60.723
Angle α, β, γ (deg.)90.00, 97.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N-terminal acetyltransferase A complex catalytic subunit ard1 / NatA complex subunit ARD1


Mass: 18452.807 Da / Num. of mol.: 2 / Fragment: amino acids 1-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: ard1, SPAC15E1.08 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UTI3, EC: 2.3.1.88
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein buffer: 25 mM sodium citrate monobasic, 200 mM NaCl, 4 mM DTT Crystallization well: 0.1 M Bis-tris, 14% Peg 3350, 18% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2011 / Details: Si(111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 41318

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: 3TFY

3tfy


Resolution: 2→28.542 Å / SU ML: 0.22 / σ(F): 1.33 / Phase error: 22.78 / Stereochemistry target values: ML / Details: PHASING WAS PERFORMED BY USING SAD AND MR
RfactorNum. reflection% reflection
Rfree0.2173 1025 4.99 %
Rwork0.1772 --
obs0.1792 41318 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 0 102 262 2826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092628
X-RAY DIFFRACTIONf_angle_d1.2573562
X-RAY DIFFRACTIONf_dihedral_angle_d20.7431076
X-RAY DIFFRACTIONf_chiral_restr0.086370
X-RAY DIFFRACTIONf_plane_restr0.013442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.997-2.04350.30341190.25042212X-RAY DIFFRACTION82
2.0435-2.09460.29031340.21892615X-RAY DIFFRACTION98
2.0946-2.15120.32381420.20162677X-RAY DIFFRACTION99
2.1512-2.21450.2281390.20062628X-RAY DIFFRACTION99
2.2145-2.28590.24661370.18742627X-RAY DIFFRACTION99
2.2859-2.36760.32411380.18312613X-RAY DIFFRACTION99
2.3676-2.46230.26071440.18862672X-RAY DIFFRACTION99
2.4623-2.57430.23421420.18892656X-RAY DIFFRACTION99
2.5743-2.70990.24871380.18472650X-RAY DIFFRACTION100
2.7099-2.87960.26591390.17922665X-RAY DIFFRACTION100
2.8796-3.10160.20261370.18022649X-RAY DIFFRACTION100
3.1016-3.41330.20781410.17012682X-RAY DIFFRACTION100
3.4133-3.90620.16891360.15652612X-RAY DIFFRACTION100
3.9062-4.91730.14761370.1362657X-RAY DIFFRACTION99
4.9173-28.54540.17331400.18742640X-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)
10.8003-0.4378-0.17532.16260.08682.0010.0190.0122-0.0105-0.01380.0551-0.11320.0351-0.0537-0.06580.06920.0011-0.00490.08770.00650.108718.26148.74227.8134
22.0455-0.47770.03491.86571.17483.16170.0299-0.04770.1594-0.0575-0.03970.1383-0.1533-0.45860.00730.14690.0294-0.00410.20870.03870.15465.499312.148524.7469
31.22730.3992-0.36642.27470.24372.0988-0.0653-0.04510.09020.10870.1363-0.1182-0.00050.1163-0.05650.1240.009-0.0020.1030.00180.09721.49533.55282.7243
41.29110.08060.20951.98971.75483.7401-0.02090.0278-0.15360.1853-0.17510.22820.3319-0.31990.17840.1746-0.02380.02590.18730.01020.16628.420330.05792.2589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:88)
2X-RAY DIFFRACTION2(chain A and resid 89:153)
3X-RAY DIFFRACTION3(chain B and resid 2:88)
4X-RAY DIFFRACTION4(chain B and resid 89:153)

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