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- PDB-5n1w: Structure of xEco2 acetyltransferase domain bound to K105-CoA con... -

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Basic information

Entry
Database: PDB / ID: 5n1w
TitleStructure of xEco2 acetyltransferase domain bound to K105-CoA conjugate
Components
  • ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA
  • XEco2
KeywordsCELL CYCLE
Function / homology
Function and homology information


meiotic cohesin complex / mitotic cohesin complex / mitotic sister chromatid cohesion / protein-lysine-acetyltransferase activity / regulation of DNA replication / chromosome, centromeric region / meiotic cell cycle / double-stranded DNA binding / cell division / DNA repair ...meiotic cohesin complex / mitotic cohesin complex / mitotic sister chromatid cohesion / protein-lysine-acetyltransferase activity / regulation of DNA replication / chromosome, centromeric region / meiotic cell cycle / double-stranded DNA binding / cell division / DNA repair / chromatin / ATP hydrolysis activity / zinc ion binding / ATP 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 / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain ...N-acetyltransferase ESCO, zinc-finger / N-acetyltransferase ESCO, acetyl-transferase domain / zinc-finger of acetyl-transferase ESCO / ESCO1/2 acetyl-transferase / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-8HB / XEco2 / Structural maintenance of chromosomes protein 3
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XEco2
B: XEco2
C: ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA
D: ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8168
Polymers43,0884
Non-polymers1,7284
Water2,810156
1
A: XEco2
D: ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4084
Polymers21,5442
Non-polymers8642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-11 kcal/mol
Surface area10880 Å2
MethodPISA
2
B: XEco2
C: ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4084
Polymers21,5442
Non-polymers8642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-8 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.301, 60.610, 66.905
Angle α, β, γ (deg.)90.00, 99.63, 90.00
Int Tables number4
Space group name H-MP1211

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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: Protein/peptide ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA


Mass: 687.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: O93309*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-8HB / (2~{S})-2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]propanoic acid


Mass: 839.597 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40N7O18P3S / Source: (synth.) Xenopus laevis (African clawed frog)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 40% ethylene glycol, 0.1 M HEPES pH 7.5, 5% PEG 3K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 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: 2.3→56.493 Å / Num. obs: 20265 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.2701 / Net I/σ(I): 6.78
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.834 / Mean I/σ(I) obs: 2.02 / Num. unique all: 2010 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2664: ???)refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MXE

4mxe


Resolution: 2.3→56.493 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.63
RfactorNum. reflection% reflection
Rfree0.2391 988 4.88 %
Rwork0.1973 --
obs0.1995 20228 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→56.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 2 156 3007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182927
X-RAY DIFFRACTIONf_angle_d1.4223957
X-RAY DIFFRACTIONf_dihedral_angle_d14.9141739
X-RAY DIFFRACTIONf_chiral_restr0.064438
X-RAY DIFFRACTIONf_plane_restr0.008484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.42130.36891370.30452716X-RAY DIFFRACTION100
2.4213-2.5730.30231210.25862764X-RAY DIFFRACTION100
2.573-2.77160.25591440.22472712X-RAY DIFFRACTION100
2.7716-3.05050.24381360.19132740X-RAY DIFFRACTION100
3.0505-3.49190.20671480.1822742X-RAY DIFFRACTION100
3.4919-4.39920.19821340.15382768X-RAY DIFFRACTION100
4.3992-56.51030.24521680.19772798X-RAY DIFFRACTION100

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