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- PDB-5hh0: Crystal structure of human Naa60 in complex with CoA -

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Basic information

Entry
Database: PDB / ID: 5hh0
TitleCrystal structure of human Naa60 in complex with CoA
ComponentsN-alpha-acetyltransferase 60
KeywordsTRANSFERASE / N-terminal acetylation / NATs / Protein modification
Function / homology
Function and homology information


N-terminal methionine Nalpha-acetyltransferase NatF / N-terminal peptidyl-methionine acetylation / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / histone acetyltransferase activity / histone acetyltransferase / chromosome segregation / nucleosome assembly / cell population proliferation ...N-terminal methionine Nalpha-acetyltransferase NatF / N-terminal peptidyl-methionine acetylation / N-terminal protein amino acid acetylation / peptide alpha-N-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) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
COENZYME A / N-alpha-acetyltransferase 60
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChen, J.Y. / Liu, L. / Yun, C.H.
Funding support China, 3items
OrganizationGrant numberCountry
National Basic Research Program of China2012CB917202 China
National Science Foundation of China31270769 China
Ministry of Science and Technology of ChinaNCET-12-0013 China
CitationJournal: Sci Rep / Year: 2016
Title: Structure and function of human Naa60 (NatF), a Golgi-localized bi-functional acetyltransferase
Authors: Chen, J.Y. / Liu, L. / Cao, C.L. / Li, M.J. / Tan, K. / Yang, X. / Yun, C.H.
History
DepositionJan 9, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-alpha-acetyltransferase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7362
Polymers22,9681
Non-polymers7681
Water4,648258
1
A: N-alpha-acetyltransferase 60
hetero molecules

A: N-alpha-acetyltransferase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4714
Polymers45,9362
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4970 Å2
ΔGint-16 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.100, 73.437, 43.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 22968.012 Da / Num. of mol.: 1 / Fragment: UNP residues 1-199 / Mutation: V4E, V5E, P6R
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 / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293.15 K / Method: liquid diffusion / pH: 7.5
Details: 0.2 M L-Proline, 0.1 M HEPES pH7.5, 10% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 28597 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 31.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data processing
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HGZ

5hgz


Resolution: 1.6→33.55 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1839 1454 5.09 %
Rwork0.1812 --
obs0.1814 28588 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→33.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 48 258 1868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171719
X-RAY DIFFRACTIONf_angle_d1.6512354
X-RAY DIFFRACTIONf_dihedral_angle_d20.779699
X-RAY DIFFRACTIONf_chiral_restr0.237265
X-RAY DIFFRACTIONf_plane_restr0.008282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6005-1.65770.32161290.28852542X-RAY DIFFRACTION95
1.6577-1.7240.28291430.25912677X-RAY DIFFRACTION100
1.724-1.80250.30711390.24182696X-RAY DIFFRACTION100
1.8025-1.89750.23171570.23212678X-RAY DIFFRACTION100
1.8975-2.01640.20971400.20782710X-RAY DIFFRACTION100
2.0164-2.17210.21711470.19942731X-RAY DIFFRACTION100
2.1721-2.39060.20581460.1942717X-RAY DIFFRACTION100
2.3906-2.73640.18181440.19262744X-RAY DIFFRACTION100
2.7364-3.4470.17751560.17872771X-RAY DIFFRACTION100
3.447-33.55740.14741530.15022868X-RAY DIFFRACTION98

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