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- PDB-5n1u: Structure of xEco2 acetyltransferase domain -

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Basic information

Entry
Database: PDB / ID: 5n1u
TitleStructure of xEco2 acetyltransferase domain
ComponentsXEco2
KeywordsCELL CYCLE
Function / homology
Function and homology information


protein-lysine-acetyltransferase activity / mitotic sister chromatid cohesion / chromatin / zinc ion binding / nucleus
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
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.976 Å
AuthorsChao, W.C.H. / Wade, B.O. / Singleton, M.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKFC001155 United Kingdom
Wellcome TrustFC001155 United Kingdom
Medical Research Council (United Kingdom)FC001155 United Kingdom
CitationJournal: Sci Rep / Year: 2017
Title: Structural Basis of Eco1-Mediated Cohesin Acetylation.
Authors: Chao, W.C. / Wade, B.O. / Bouchoux, C. / Jones, A.W. / Purkiss, A.G. / Federico, S. / O'Reilly, N. / Snijders, A.P. / Uhlmann, F. / Singleton, M.R.
History
DepositionFeb 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XEco2
B: XEco2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2474
Polymers41,7122
Non-polymers1,5352
Water00
1
A: XEco2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6242
Polymers20,8561
Non-polymers7681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: XEco2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6242
Polymers20,8561
Non-polymers7681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.475, 66.287, 109.763
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and ((resid 524 and (name N or name...
21(chain D and ((resid 524 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain C and ((resid 524 and (name N or name...C524
121(chain C and ((resid 524 and (name N or name...C201 - 202
131(chain C and ((resid 524 and (name N or name...C201 - 202
141(chain C and ((resid 524 and (name N or name...C201 - 202
151(chain C and ((resid 524 and (name N or name...C201 - 202
211(chain D and ((resid 524 and (name N or name...D524
221(chain D and ((resid 524 and (name N or name...D0
231(chain D and ((resid 524 and (name N or name...D0
241(chain D and ((resid 524 and (name N or name...D0
251(chain D and ((resid 524 and (name N or name...D0

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Components

#1: Protein XEco2


Mass: 20856.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: xeco2 / Production host: Escherichia coli (E. coli) / References: UniProt: A8QZK6
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M NaCl, 0.1 M imidazole pH 7 and 0.864 M ammonium phosphate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.976→28.834 Å / Num. obs: 9148 / % possible obs: 99 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.2968 / Net I/σ(I): 7.7
Reflection shellResolution: 2.98→3.08 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 1.52 / Num. measured obs: 860

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MXE

4mxe


Resolution: 2.976→28.834 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.12
RfactorNum. reflection% reflection
Rfree0.2676 908 9.99 %
Rwork0.2234 --
obs0.2279 9090 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 293.9 Å2 / Biso mean: 72.81 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.976→28.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 160 0 2789
Biso mean--66.25 --
Num. residues----340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032788
X-RAY DIFFRACTIONf_angle_d0.6883794
X-RAY DIFFRACTIONf_chiral_restr0.046426
X-RAY DIFFRACTIONf_plane_restr0.004465
X-RAY DIFFRACTIONf_dihedral_angle_d18.0911692
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1629X-RAY DIFFRACTION11.018TORSIONAL
12B1629X-RAY DIFFRACTION11.018TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.976-3.16220.34281400.33141279141995
3.1622-3.4060.34941500.293713441494100
3.406-3.74810.31811500.27041352150299
3.7481-4.2890.27791510.200413621513100
4.289-5.39780.20891550.182913871542100
5.3978-28.83530.25281620.21331458162099

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