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- PDB-4lx9: Archaeal amino-terminal acetyltransferase (NAT) bound to acetyl c... -

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Basic information

Entry
Database: PDB / ID: 4lx9
TitleArchaeal amino-terminal acetyltransferase (NAT) bound to acetyl coenzyme A
ComponentsARCHAEAL AMINO-TERMINAL ACETYLTRANSFERASE
KeywordsTRANSFERASE / amino-terminal acetyltransferase / GNAT fold / amino-terminal acetyltransferase (NAT)
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 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsLiszczak, G.P. / Marmorstein, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Implications for the evolution of eukaryotic amino-terminal acetyltransferase (NAT) enzymes from the structure of an archaeal ortholog.
Authors: Liszczak, G. / Marmorstein, R.
History
DepositionJul 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: ARCHAEAL AMINO-TERMINAL ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4144
Polymers19,4741
Non-polymers9403
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.840, 35.062, 51.219
Angle α, β, γ (deg.)90.00, 100.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ARCHAEAL AMINO-TERMINAL ACETYLTRANSFERASE


Mass: 19473.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO0209 / Production host: Escherichia coli (E. coli)
References: UniProt: Q980R9, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% PEG 3350, 0.1 M zinc acetate, Protein: 7.5 mg/mL, 20 mM tris, 150 mM NaCl, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 1, 2013
RadiationMonochromator: Rigaku Osmic VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 37578 / Num. obs: 12433 / % possible obs: 98 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Redundancy: 3 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 7.66
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1223 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-3000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→21.049 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 619 5 %5%
Rwork0.1994 ---
obs0.2015 12390 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→21.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 53 147 1484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071371
X-RAY DIFFRACTIONf_angle_d1.1781862
X-RAY DIFFRACTIONf_dihedral_angle_d15.71525
X-RAY DIFFRACTIONf_chiral_restr0.078203
X-RAY DIFFRACTIONf_plane_restr0.004228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9798-2.17880.26171510.2222862X-RAY DIFFRACTION98
2.1788-2.49370.26681550.21712951X-RAY DIFFRACTION100
2.4937-3.14010.29361550.26362941X-RAY DIFFRACTION99
3.1401-21.05040.20741580.16263017X-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)
10.6827-0.12410.54050.74380.58190.6056-0.0672-0.01760.0213-0.0450.1216-0.0575-0.07130.18310.02870.0566-0.00130.00880.1490.00680.108-9.57-16.547516.1093
20.1949-0.1972-0.03040.25680.010.294-0.01990.0366-0.01580.1110.03690.0897-0.0299-0.0130.0290.1038-0.00490.00360.08590.03110.1119-24.5395-21.586716.5744
31.2231-0.16190.2740.47970.08830.4090.01280.22220.0572-0.0448-0.04890.03050.0350.038-0.04210.1146-0.0042-0.00210.09470.0160.0763-25.3-14.932411.3017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 60:110)
2X-RAY DIFFRACTION2(chain A and resid 111:145)
3X-RAY DIFFRACTION3(chain A and resid 146:216)

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