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

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Basic information

Entry
Database: PDB / ID: 5hgz
TitleCrystal structure of human Naa60 in complex with acetyl-CoA
ComponentsN-alpha-acetyltransferase 60
KeywordsTRANSFERASE / N-terminal acetylation / Complex / NATs / Protein modificaiton
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
ACETYL COENZYME *A / MALONIC ACID / N-alpha-acetyltransferase 60
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.383 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 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,7124
Polymers27,6951
Non-polymers1,0183
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-10 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.287, 57.365, 68.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 27694.500 Da / Num. of mol.: 1 / 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-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 1.9 Å3/Da / Density % sol: 35.23 %
Crystal growTemperature: 293.15 K / Method: liquid diffusion / pH: 4
Details: 10mM Tris pH 8.0, 75mM NaCl, 0.5% glycerol, 3%(v/v) Tacsimate pH4.0 (Hampton Research) and 7.5%(w/v) polyethylene glycol 3350 (PEG 3350)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.383→50 Å / Num. obs: 43682 / % possible obs: 99.8 % / Redundancy: 6.9 % / Net I/σ(I): 21.5
Reflection shellResolution: 1.383→1.42 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.383→25.814 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1918 2189 5.01 %
Rwork0.1824 --
obs0.1829 43660 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.383→25.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 65 289 2042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181884
X-RAY DIFFRACTIONf_angle_d1.5292578
X-RAY DIFFRACTIONf_dihedral_angle_d20.485772
X-RAY DIFFRACTIONf_chiral_restr0.134286
X-RAY DIFFRACTIONf_plane_restr0.009316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3828-1.41280.30991390.27862458X-RAY DIFFRACTION96
1.4128-1.44570.29731410.26032571X-RAY DIFFRACTION100
1.4457-1.48190.23591270.24462563X-RAY DIFFRACTION100
1.4819-1.52190.24371310.22422591X-RAY DIFFRACTION100
1.5219-1.56670.24551480.21812565X-RAY DIFFRACTION100
1.5667-1.61730.21861320.20882542X-RAY DIFFRACTION100
1.6173-1.6750.22051420.20612574X-RAY DIFFRACTION100
1.675-1.74210.21621090.22600X-RAY DIFFRACTION100
1.7421-1.82140.22991360.19822585X-RAY DIFFRACTION100
1.8214-1.91740.23721340.19142591X-RAY DIFFRACTION100
1.9174-2.03740.19851460.18422580X-RAY DIFFRACTION100
2.0374-2.19470.1621510.17412590X-RAY DIFFRACTION100
2.1947-2.41540.21871330.18352625X-RAY DIFFRACTION100
2.4154-2.76460.22221360.18052623X-RAY DIFFRACTION100
2.7646-3.48170.15991380.16772675X-RAY DIFFRACTION100
3.4817-25.81860.15181460.16032738X-RAY DIFFRACTION98

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