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- PDB-4x5k: Human NAA50 complex with coenzyme A and an acetylated peptide -

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Basic information

Entry
Database: PDB / ID: 4x5k
TitleHuman NAA50 complex with coenzyme A and an acetylated peptide
Components
  • ACE-MMAS
  • N-alpha-acetyltransferase 50
KeywordsTransferase/Peptide / N-acetyl transferase / GCN-5. cotranslation modification / Transferase-Peptide complex
Function / homology
Function and homology information


: / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / mitotic sister chromatid cohesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups ...: / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / mitotic sister chromatid cohesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleolus / extracellular exosome / nucleus / cytoplasm / cytosol
Similarity search - Function
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 50
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.494 Å
AuthorsReddi, R. / Addlagatta, A.
CitationJournal: To Be Published
Title: Human NAA50 with coenzymeA and a peptide
Authors: Reddi, R. / Addlagatta, A.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Advisory / Data collection / Derived calculations
Category: diffrn_detector / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-alpha-acetyltransferase 50
B: ACE-MMAS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6603
Polymers19,8922
Non-polymers7681
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-6 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.626, 53.193, 67.586
Angle α, β, γ (deg.)90.000, 90.00, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein N-alpha-acetyltransferase 50 / N-acetyltransferase 13 / N-acetyltransferase 5 / hNAT5 / N-acetyltransferase san homolog / hSAN / ...N-acetyltransferase 13 / N-acetyltransferase 5 / hNAT5 / N-acetyltransferase san homolog / hSAN / NatE catalytic subunit


Mass: 19427.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: A549 / Gene: NAA50, MAK3, NAT13, NAT5 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9GZZ1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide ACE-MMAS


Mass: 464.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-COA / COENZYME A


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


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.39→30.49 Å / Num. obs: 5836 / % possible obs: 91.2 % / Redundancy: 2.3 % / Net I/σ(I): 11.27

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OB0

2ob0


Resolution: 2.494→28.524 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 33.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 269 4.61 %
Rwork0.2019 --
obs0.2046 5836 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 2.494→28.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2521 0 100 37 2658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011328
X-RAY DIFFRACTIONf_angle_d1.3571799
X-RAY DIFFRACTIONf_dihedral_angle_d18.278496
X-RAY DIFFRACTIONf_chiral_restr0.092197
X-RAY DIFFRACTIONf_plane_restr0.005225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4944-3.14210.34711250.2701270197
3.1421-28.52560.23371440.1844286699

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