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- PDB-5wje: Crystal structure of Naa80 bound to a bisubstrate analogue -

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Basic information

Entry
Database: PDB / ID: 5wje
TitleCrystal structure of Naa80 bound to a bisubstrate analogue
Components
  • Actin N-terminus peptide
  • CG8481, isoform B
KeywordsTRANSFERASE / Acetyltransferase / acetyl-CoA / GNAT fold / acetylation
Function / homology
Function and homology information


N-terminal peptidyl-aspartic acid acetylation / N-terminal peptidyl-glutamic acid acetylation / peptide alpha-N-acetyltransferase activity / acetyl-CoA binding / N-acetyltransferase activity / protein acetylation / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytoplasm
Similarity search - Function
N-alpha-acetyltransferase 80 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
CARBOXYMETHYL COENZYME *A / N-alpha-acetyltransferase 80
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.765 Å
AuthorsGoris, M. / Magin, R.S. / Marmorstein, R. / Arnesen, T.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural determinants and cellular environment define processed actin as the sole substrate of the N-terminal acetyltransferase NAA80.
Authors: Goris, M. / Magin, R.S. / Foyn, H. / Myklebust, L.M. / Varland, S. / Ree, R. / Drazic, A. / Bhambra, P. / Stove, S.I. / Baumann, M. / Haug, B.E. / Marmorstein, R. / Arnesen, T.
History
DepositionJul 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Feb 26, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / struct_asym / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site.label_asym_id ..._atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1Oct 4, 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: CG8481, isoform B
B: Actin N-terminus peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4273
Polymers18,6022
Non-polymers8261
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint1 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.136, 64.370, 68.589
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CG8481, isoform B / FI06462p


Mass: 18127.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dmel\CG8481, CG8481-RB, CG8481, Dmel_CG8481 / Production host: Escherichia coli (E. coli)
References: UniProt: Q59DX8, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide Actin N-terminus peptide


Mass: 474.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#3: Chemical ChemComp-CMC / CARBOXYMETHYL COENZYME *A


Mass: 825.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O18P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 24% polyethylene glycol (PEG) 3350, 0.1 M Bis Tris propane (pH 7.6, pH adjusted with citric acid) and 10 mM NaBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.765→34.294 Å / Num. obs: 16748 / % possible obs: 99 % / Redundancy: 10.5 % / Biso Wilson estimate: 22.86 Å2 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.041 / Rrim(I) all: 0.137 / Χ2: 0.992 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.765-1.86.40.86915580.6750.360.9450.48180.5
1.8-1.838.40.8080.8820.290.8590.501100
1.83-1.879.70.7640.9210.2560.8070.524100
1.87-1.9110.30.7590.930.2450.7980.55100
1.91-1.9510.70.6220.9360.1980.6540.636100
1.95-1.9910.80.5650.9490.1790.5940.597100
1.99-2.0410.40.4440.9570.1440.4670.63100
2.04-2.110.80.4010.9670.1260.4210.703100
2.1-2.1611.10.3220.9820.10.3370.688100
2.16-2.2311.40.2910.980.0890.3040.733100
2.23-2.3111.30.260.9860.080.2720.845100
2.31-2.4110.2220.9870.0690.2330.836100
2.4-2.5110.60.1980.9880.0630.2080.918100
2.51-2.6410.90.170.990.0530.1781.034100
2.64-2.8111.30.1540.9930.0480.1611.094100
2.81-3.0311.10.1270.9930.040.1331.308100
3.03-3.3310.50.1040.9950.0330.1091.611100
3.33-3.8111.10.0860.9960.0270.0911.867100
3.81-4.810.50.0720.9970.0230.0761.96399.9
4.8-50100.0650.9980.0210.0681.66899.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WJD

5wjd


Resolution: 1.765→34.294 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.33 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.2175 1667 10 %
Rwork0.1769 15003 -
obs0.1809 16670 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.38 Å2 / Biso mean: 24.3257 Å2 / Biso min: 12.72 Å2
Refinement stepCycle: final / Resolution: 1.765→34.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 52 162 1493
Biso mean--28.09 30.9 -
Num. residues----163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021364
X-RAY DIFFRACTIONf_angle_d0.6411851
X-RAY DIFFRACTIONf_chiral_restr0.042204
X-RAY DIFFRACTIONf_plane_restr0.003228
X-RAY DIFFRACTIONf_dihedral_angle_d10.6261142
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.765-1.81740.26811260.25511155128194
1.8174-1.8760.28031340.247612291363100
1.876-1.94310.26921430.245612381381100
1.9431-2.02090.25221390.22612341373100
2.0209-2.11280.22451270.207912451372100
2.1128-2.22420.22631420.20312371379100
2.2242-2.36350.21031430.204912371380100
2.3635-2.54590.22051340.203112491383100
2.5459-2.8020.23261470.190112581405100
2.802-3.20720.24991370.178612641401100
3.2072-4.03980.1951420.13612931435100
4.0398-34.3010.18061530.138413641517100

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