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- PDB-6sp0: Structure of Esco2 acetyltransferase in complex with CoA -

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Basic information

Entry
Database: PDB / ID: 6sp0
TitleStructure of Esco2 acetyltransferase in complex with CoA
ComponentsN-acetyltransferase ESCO2
KeywordsTRANSFERASE / Acetyltransferase / Zinc finger / Coenzyme A
Function / homology
Function and homology information


post-translational protein acetylation / Establishment of Sister Chromatid Cohesion / chromocenter / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / XY body / sister chromatid cohesion / regulation of DNA replication / acetyltransferase activity / hematopoietic progenitor cell differentiation / pericentric heterochromatin ...post-translational protein acetylation / Establishment of Sister Chromatid Cohesion / chromocenter / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / XY body / sister chromatid cohesion / regulation of DNA replication / acetyltransferase activity / hematopoietic progenitor cell differentiation / pericentric heterochromatin / protein localization to chromatin / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / chromosome segregation / double-strand break repair / cell junction / chromosome / site of double-strand break / chromatin / Golgi apparatus / nucleoplasm / metal ion binding
Similarity search - Function
N-acetyltransferase ESCO, zinc-finger / N-acetyltransferase ESCO, acetyl-transferase domain / zinc-finger of acetyl-transferase ESCO / ESCO1/2 acetyl-transferase
Similarity search - Domain/homology
COENZYME A / N-acetyltransferase ESCO2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsDe, I. / Pena, V.
CitationJournal: Sci Rep / Year: 2020
Title: Alternative catalytic residues in the active site of Esco acetyltransferases
Authors: Ajam, T. / De, I. / Petkau, N. / Whelan, G. / Pena, V. / Eichele, G.
History
DepositionAug 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: N-acetyltransferase ESCO2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8463
Polymers26,0131
Non-polymers8332
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint0 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.680, 52.680, 107.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw

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Components

#1: Protein N-acetyltransferase ESCO2 / Establishment of cohesion 1 homolog 2 / ECO1 homolog 2


Mass: 26013.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Esco2 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q8CIB9, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
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: 3.26 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris, 20% (v/v) and 2-Methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→47.3 Å / Num. obs: 28388 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.99 / Net I/σ(I): 15.2
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1533 / CC1/2: 0.928 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→37.62 Å / SU ML: 0.2091 / Cross valid method: FREE R-VALUE / Phase error: 20.6851
RfactorNum. reflection% reflection
Rfree0.198 1991 7.02 %
Rwork0.169 --
obs-28343 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37 Å2
Refinement stepCycle: LAST / Resolution: 1.77→37.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 49 158 1813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211696
X-RAY DIFFRACTIONf_angle_d1.23562301
X-RAY DIFFRACTIONf_chiral_restr0.0694250
X-RAY DIFFRACTIONf_plane_restr0.0084286
X-RAY DIFFRACTIONf_dihedral_angle_d12.4111997
LS refinement shell
Resolution (Å)Num. reflection RfreeNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.791271646X-RAY DIFFRACTION90.41
1.79-1.821401948X-RAY DIFFRACTION99.9
1.82-1.841401792X-RAY DIFFRACTION99.74
1.84-1.861401874X-RAY DIFFRACTION99.75
1.86-1.891401859X-RAY DIFFRACTION99.9
1.89-1.921301888X-RAY DIFFRACTION99.9
1.92-1.951421874X-RAY DIFFRACTION100
1.95-1.981401828X-RAY DIFFRACTION100
1.98-2.021441869X-RAY DIFFRACTION99.85
2.02-2.051421828X-RAY DIFFRACTION99.95
2.05-2.091421901X-RAY DIFFRACTION99.8
2.09-2.131471860X-RAY DIFFRACTION99.9
2.13-2.181421901X-RAY DIFFRACTION100
2.18-2.231301807X-RAY DIFFRACTION99.95
2.23-2.291461877X-RAY DIFFRACTION99.95
2.29-2.351441874X-RAY DIFFRACTION100
2.35-2.421441862X-RAY DIFFRACTION99.85
2.42-2.51481860X-RAY DIFFRACTION100
2.5-2.591381851X-RAY DIFFRACTION99.8
2.59-2.691441851X-RAY DIFFRACTION99.75
2.69-2.811381877X-RAY DIFFRACTION99.9
2.81-2.961481864X-RAY DIFFRACTION99.6
2.96-3.151341833X-RAY DIFFRACTION99.14
3.15-3.391311873X-RAY DIFFRACTION99.8
3.39-3.731451880X-RAY DIFFRACTION99.75
3.73-4.271421824X-RAY DIFFRACTION99.75
4.27-5.371391885X-RAY DIFFRACTION99.66

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