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- PDB-4u9v: Crystal structure of NatD (Naa40p) bound to acetyl CoA -

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Basic information

Entry
Database: PDB / ID: 4u9v
TitleCrystal structure of NatD (Naa40p) bound to acetyl CoA
ComponentsN-alpha-acetyltransferase 40
KeywordsTRANSFERASE / Acetyltransferase / GNAT fold / N-terminal acetylation / acetyl-CoA
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
ACETYL COENZYME *A / N-alpha-acetyltransferase 40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsMagin, R.S. / Liszczak, G.P. / Marmorstein, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM060293 United States
CitationJournal: Structure / Year: 2015
Title: The Molecular Basis for Histone H4- and H2A-Specific Amino-Terminal Acetylation by NatD.
Authors: Magin, R.S. / Liszczak, G.P. / Marmorstein, R.
History
DepositionAug 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.4Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: N-alpha-acetyltransferase 40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7202
Polymers22,9101
Non-polymers8101
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.256, 44.064, 50.356
Angle α, β, γ (deg.)90.000, 95.440, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-484-

HOH

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Components

#1: Protein N-alpha-acetyltransferase 40 / N-acetyltransferase 11 / NatD catalytic subunit


Mass: 22910.037 Da / Num. of mol.: 1 / Fragment: UNP residues 4-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA40, NAT11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86UY6, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 3350, 100 mM sodium citrate tribasic dihydrate, 100 mM citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2013
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 18521 / % possible obs: 98.5 % / Redundancy: 8.1 % / Biso Wilson estimate: 19.21 Å2 / Rmerge(I) obs: 0.074 / Χ2: 0.805 / Net I/av σ(I): 22.629 / Net I/σ(I): 7 / Num. measured all: 150300
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.78-1.844.20.47116430.57287.5
1.84-1.9260.39618230.57997.9
1.92-27.60.30818390.65599.8
2-2.118.50.22818900.72100
2.11-2.249.10.17118620.73100
2.24-2.428.90.13218640.823100
2.42-2.669.10.10118720.817100
2.66-3.049.30.07418960.877100
3.04-3.8390.04718900.914100
3.83-5090.03519421.073100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data collection
HKL-2000data reduction
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UA3

4ua3


Resolution: 1.78→43.929 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 1768 4.98 %
Rwork0.1674 33723 -
obs0.1693 35491 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.21 Å2 / Biso mean: 24.7146 Å2 / Biso min: 9.73 Å2
Refinement stepCycle: final / Resolution: 1.78→43.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1582 0 51 166 1799
Biso mean--21.59 32.57 -
Num. residues----197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091671
X-RAY DIFFRACTIONf_angle_d1.1262260
X-RAY DIFFRACTIONf_chiral_restr0.045235
X-RAY DIFFRACTIONf_plane_restr0.004285
X-RAY DIFFRACTIONf_dihedral_angle_d15.645605
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.8220.31231000.28921998209874
1.822-1.87560.25951230.24832423254691
1.8756-1.93610.24381400.20722613275398
1.9361-2.00530.22231410.19272641278299
2.0053-2.08560.21011380.179526912829100
2.0856-2.18050.22181380.160826352773100
2.1805-2.29550.21981410.170826992840100
2.2955-2.43930.20831410.169626522793100
2.4393-2.62760.23621420.175126922834100
2.6276-2.8920.24051440.173926562800100
2.892-3.31030.18511370.16226822819100
3.3103-4.17010.18021420.135426742816100
4.1701-43.94280.17081410.151626672808100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.640.0825-0.28971.29630.29822.5249-0.03020.1527-0.046-0.0295-0.02720.02320.0955-0.13910.03710.0981-0.0038-0.00690.1242-0.00270.13139.90623.012415.7482
21.66870.14980.45651.9497-0.5481.8355-0.05290.0309-0.2194-0.0415-0.1109-0.27220.21950.37170.13170.1580.0130.03470.15610.01790.224226.98593.691118.1491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 24:168)B24 - 168
2X-RAY DIFFRACTION2(chain B and resid 169:220)B169 - 220

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