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- PDB-5wjd: Crystal structure of Naa80 bound to acetyl-CoA -

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Basic information

Entry
Database: PDB / ID: 5wjd
TitleCrystal structure of Naa80 bound to acetyl-CoA
ComponentsCG8481, 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 / acetyl-CoA binding / peptide alpha-N-acetyltransferase activity / N-acetyltransferase activity / 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
ACETYL COENZYME *A / CITRIC ACID / N-alpha-acetyltransferase 80
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 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 1.3Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1293
Polymers18,1271
Non-polymers1,0022
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.685, 62.643, 63.758
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: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.31 Å3/Da / Density % sol: 46.85 %
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: 2→50 Å / Num. obs: 11715 / % possible obs: 99.5 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.052 / Rrim(I) all: 0.185 / Χ2: 1.468 / Net I/σ(I): 4.7 / Num. measured all: 144411
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.03100.7565750.7790.2450.7970.77799.8
2.03-2.0711.10.7075510.8580.2180.7410.79398
2.07-2.1111.10.6755680.8830.2080.7070.84599.8
2.11-2.1512.40.5615830.940.1640.5850.87998.6
2.15-2.212.80.5345620.9270.1540.5560.95698.6
2.2-2.2512.90.5125700.9370.1460.5320.994100
2.25-2.31130.4475840.9550.1280.4651.05399
2.31-2.3712.70.4375610.9640.1260.4550.9898.9
2.37-2.4412.10.3585940.9590.1070.3741.124100
2.44-2.5212.90.3385610.9710.0970.3521.21999.3
2.52-2.6112.60.295920.9730.0850.3031.31599.5
2.61-2.7113.30.2765690.9810.0780.2871.32899.5
2.71-2.8413.10.2365890.9850.0680.2461.37499.5
2.84-2.9912.90.1985960.9860.0570.2071.59599.7
2.99-3.1712.20.1735830.9890.0510.1811.98799.7
3.17-3.4212.70.1425880.9910.0410.1482.34199.7
3.42-3.76130.126030.9960.0350.1252.421100
3.76-4.3112.50.1025930.9960.030.1062.573100
4.31-5.43120.0886210.9960.0260.0922.329100
5.43-5011.50.086720.9980.0240.0841.98599.9

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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: 2CNM

2cnm


Resolution: 2.001→44.684 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2223 1174 10.05 %
Rwork0.1836 10507 -
obs0.1876 11681 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.41 Å2 / Biso mean: 25.5361 Å2 / Biso min: 10.94 Å2
Refinement stepCycle: final / Resolution: 2.001→44.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 64 129 1413
Biso mean--31.97 33.39 -
Num. residues----157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031313
X-RAY DIFFRACTIONf_angle_d0.7441785
X-RAY DIFFRACTIONf_chiral_restr0.045197
X-RAY DIFFRACTIONf_plane_restr0.003219
X-RAY DIFFRACTIONf_dihedral_angle_d9.966780
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0006-2.09160.28531420.21191259140197
2.0916-2.20190.26651420.19931272141499
2.2019-2.33990.23771430.192512911434100
2.3399-2.52050.24241420.1911298144099
2.5205-2.77410.24991490.195913091458100
2.7741-3.17550.22211440.186913241468100
3.1755-4.00030.18591490.158813431492100
4.0003-44.69540.20491630.18314111574100

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