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- PDB-5icw: Crystal structure of human NatF (hNaa60) homodimer bound to Coenzyme A -

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Basic information

Entry
Database: PDB / ID: 5icw
TitleCrystal structure of human NatF (hNaa60) homodimer bound to Coenzyme A
ComponentsN-alpha-acetyltransferase 60
KeywordsTRANSFERASE / Acetylation / GNAT / NAT
Function / homology
Function and homology information


N-terminal peptidyl-methionine acetylation / N-terminal methionine Nalpha-acetyltransferase NatF / N-terminal protein amino acid acetylation / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / histone H4 acetyltransferase activity / histone acetyltransferase activity / histone acetyltransferase / chromosome segregation / nucleosome assembly ...N-terminal peptidyl-methionine acetylation / N-terminal methionine Nalpha-acetyltransferase NatF / N-terminal protein amino acid acetylation / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / histone H4 acetyltransferase activity / histone acetyltransferase activity / histone acetyltransferase / chromosome segregation / nucleosome assembly / cell population proliferation / Golgi membrane / protein homodimerization activity
Similarity search - Function
N-alpha-acetyltransferase 60-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 60
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsStove, S.I. / Magin, R.S. / Marmorstein, R. / Arnesen, T.
Funding support Norway, United States, 6items
OrganizationGrant numberCountry
Norwegian Cancer Society Norway
Bergen Research Foundaton (BFS) Norway
The Research Council of Norway Norway
Western Norway Regional Health Authority Norway
National Institutes of HealthGM060293 United States
National Institutes of HealthGM071339 United States
CitationJournal: Structure / Year: 2016
Title: Crystal Structure of the Golgi-Associated Human N alpha-Acetyltransferase 60 Reveals the Molecular Determinants for Substrate-Specific Acetylation.
Authors: Stve, S.I. / Magin, R.S. / Foyn, H. / Haug, B.E. / Marmorstein, R. / Arnesen, T.
History
DepositionFeb 23, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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: N-alpha-acetyltransferase 60
B: N-alpha-acetyltransferase 60
C: N-alpha-acetyltransferase 60
D: N-alpha-acetyltransferase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,28212
Polymers83,0704
Non-polymers3,2128
Water8,359464
1
A: N-alpha-acetyltransferase 60
B: N-alpha-acetyltransferase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1416
Polymers41,5352
Non-polymers1,6064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-39 kcal/mol
Surface area17710 Å2
MethodPISA
2
C: N-alpha-acetyltransferase 60
hetero molecules

D: N-alpha-acetyltransferase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1416
Polymers41,5352
Non-polymers1,6064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area4760 Å2
ΔGint-41 kcal/mol
Surface area17570 Å2
MethodPISA
3
D: N-alpha-acetyltransferase 60
hetero molecules

C: N-alpha-acetyltransferase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1416
Polymers41,5352
Non-polymers1,6064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area4760 Å2
ΔGint-41 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.840, 84.298, 68.485
Angle α, β, γ (deg.)90.00, 91.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
N-alpha-acetyltransferase 60 / Histone acetyltransferase type B protein 4 / HAT4 / N-acetyltransferase 15 / NatF catalytic subunit


Mass: 20767.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA60, HAT4, NAT15, UNQ2771/PRO7155 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H7X0, histone acetyltransferase, EC: 2.3.1.88
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 3% Tascimate, 0.1 M Bistris pH 6.5 and 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2014
RadiationMonochromator: Rigaku Osmic VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.951→46.458 Å / Num. obs: 52859 / % possible obs: 94.63 % / Redundancy: 13 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.82
Reflection shellResolution: 1.951→1.989 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LX9

4lx9


Resolution: 1.951→46.249 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 2477 4.95 %
Rwork0.2072 --
obs0.2095 50014 94.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.951→46.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5697 0 196 464 6357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086049
X-RAY DIFFRACTIONf_angle_d1.2788243
X-RAY DIFFRACTIONf_dihedral_angle_d13.0122115
X-RAY DIFFRACTIONf_chiral_restr0.056925
X-RAY DIFFRACTIONf_plane_restr0.0051003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9512-1.98870.3416930.29611690X-RAY DIFFRACTION61
1.9887-2.02930.3175940.2952066X-RAY DIFFRACTION74
2.0293-2.07340.32361370.27842361X-RAY DIFFRACTION85
2.0734-2.12160.31341190.26662626X-RAY DIFFRACTION94
2.1216-2.17470.30031460.26392694X-RAY DIFFRACTION98
2.1747-2.23350.29951400.25932767X-RAY DIFFRACTION99
2.2335-2.29920.31891650.25242785X-RAY DIFFRACTION100
2.2992-2.37340.30041450.22392762X-RAY DIFFRACTION100
2.3734-2.45820.22281390.21592802X-RAY DIFFRACTION100
2.4582-2.55670.30131590.22062749X-RAY DIFFRACTION100
2.5567-2.6730.24631400.21922760X-RAY DIFFRACTION100
2.673-2.81390.26851350.2222795X-RAY DIFFRACTION100
2.8139-2.99020.24261520.20182780X-RAY DIFFRACTION100
2.9902-3.2210.23131460.20142774X-RAY DIFFRACTION99
3.221-3.5450.24311420.19072791X-RAY DIFFRACTION99
3.545-4.05780.21231370.17492773X-RAY DIFFRACTION99
4.0578-5.11130.1931400.16642750X-RAY DIFFRACTION98
5.1113-46.26240.29691480.19862812X-RAY DIFFRACTION98

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