[English] 日本語
Yorodumi
- PDB-5n1u: Structure of xEco2 acetyltransferase domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


mitotic sister chromatid cohesion / protein-lysine-acetyltransferase activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more