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- PDB-7kd7: Crystal structure of human NatD (NAA40) bound to a bisubstrate an... -

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Basic information

Entry
Database: PDB / ID: 7kd7
TitleCrystal structure of human NatD (NAA40) bound to a bisubstrate analogue
Components
  • N-alpha-acetyltransferase 40
  • SER-GLY-ARG-GLY-LYS
KeywordsTRANSFERASE / NatD / NAA40 / Bi-substrate
Function / homology
Function and homology information


N-terminal L-serine Nalpha-acetyltransferase NatD / histone H2A acetyltransferase activity / peptide-serine-alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / centriolar satellite / lipid metabolic process / nucleoplasm / nucleus / cytosol
Similarity search - Function
N-alpha-acetyltransferase 40 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
CARBOXYMETHYL COENZYME *A / AMINO GROUP / N-alpha-acetyltransferase 40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsDeng, S. / Marmorstein, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118090 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Novel Bisubstrate Inhibitors for Protein N-Terminal Acetyltransferase D.
Authors: Deng, Y. / Deng, S. / Ho, Y.H. / Gardner, S.M. / Huang, Z. / Marmorstein, R. / Huang, R.
History
DepositionOct 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 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
D: N-alpha-acetyltransferase 40
E: SER-GLY-ARG-GLY-LYS
A: N-alpha-acetyltransferase 40
B: SER-GLY-ARG-GLY-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,05217
Polymers48,4074
Non-polymers2,64513
Water6,648369
1
D: N-alpha-acetyltransferase 40
E: SER-GLY-ARG-GLY-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,72710
Polymers24,2032
Non-polymers1,5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-25 kcal/mol
Surface area10260 Å2
MethodPISA
2
A: N-alpha-acetyltransferase 40
B: SER-GLY-ARG-GLY-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3257
Polymers24,2032
Non-polymers1,1225
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-9 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.433, 74.349, 126.821
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 4 molecules DAEB

#1: Protein N-alpha-acetyltransferase 40 / N-acetyltransferase 11 / N-alpha-acetyltransferase D / hNatD / Protein acetyltransferase 1


Mass: 23697.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA40, NAT11, PATT1 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q86UY6, N-terminal L-serine Nalpha-acetyltransferase NatD
#2: Protein/peptide SER-GLY-ARG-GLY-LYS


Mass: 505.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 6 types, 382 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Chemical ChemComp-CMC / CARBOXYMETHYL COENZYME *A


Mass: 825.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NH2 / AMINO GROUP / Amine


Mass: 16.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NH2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 100 mM BIS-TRIS pH 5.5, 2000 mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.44→126.82 Å / Num. obs: 79927 / % possible obs: 99.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 18.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.045 / Net I/σ(I): 23.1
Reflection shellResolution: 1.44→1.46 Å / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3775 / CC1/2: 0.779

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U9W

4u9w


Resolution: 1.44→63.41 Å / SU ML: 0.1305 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.805 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1829 4010 5.02 %
Rwork0.1614 75834 -
obs0.1625 79844 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.74 Å2
Refinement stepCycle: LAST / Resolution: 1.44→63.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 162 369 3820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01833517
X-RAY DIFFRACTIONf_angle_d1.58694742
X-RAY DIFFRACTIONf_chiral_restr0.1045488
X-RAY DIFFRACTIONf_plane_restr0.0103593
X-RAY DIFFRACTIONf_dihedral_angle_d18.17771261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.460.27091230.24292506X-RAY DIFFRACTION94.98
1.46-1.470.23631260.22262531X-RAY DIFFRACTION98.08
1.47-1.490.28521360.20792548X-RAY DIFFRACTION97.78
1.49-1.510.21431390.20082569X-RAY DIFFRACTION98.26
1.51-1.530.24741540.19692515X-RAY DIFFRACTION98.74
1.53-1.550.21971290.19432567X-RAY DIFFRACTION97.97
1.55-1.580.16781100.18632585X-RAY DIFFRACTION98.72
1.58-1.60.19561200.17352623X-RAY DIFFRACTION99.13
1.6-1.630.19961490.17512538X-RAY DIFFRACTION98.42
1.63-1.660.21711330.17142628X-RAY DIFFRACTION99.03
1.66-1.690.23091160.17492587X-RAY DIFFRACTION99.59
1.69-1.720.1931400.17542625X-RAY DIFFRACTION99.6
1.72-1.750.20011280.17432585X-RAY DIFFRACTION99.6
1.75-1.790.2041470.17492629X-RAY DIFFRACTION99.82
1.79-1.830.21141400.16392581X-RAY DIFFRACTION99.85
1.83-1.880.21871270.17412638X-RAY DIFFRACTION99.96
1.88-1.930.1721560.1612611X-RAY DIFFRACTION99.89
1.93-1.990.16671540.15652589X-RAY DIFFRACTION99.75
1.99-2.050.18291600.15652601X-RAY DIFFRACTION99.68
2.05-2.130.17631380.15442627X-RAY DIFFRACTION99.71
2.13-2.210.18991390.15672627X-RAY DIFFRACTION99.89
2.21-2.310.16291330.1472645X-RAY DIFFRACTION99.78
2.31-2.430.17261560.15012633X-RAY DIFFRACTION100
2.43-2.590.15681480.14812661X-RAY DIFFRACTION99.93
2.59-2.780.15651730.15452604X-RAY DIFFRACTION99.86
2.78-3.060.17191450.16142674X-RAY DIFFRACTION100
3.06-3.510.16231360.15692706X-RAY DIFFRACTION99.96
3.51-4.420.17041320.13742712X-RAY DIFFRACTION99.34
4.42-63.410.21941230.17972889X-RAY DIFFRACTION99.7

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