5GOB

Lys6-linked di-ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.153 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Monomer/Oligomer Quasi-Racemic Protein Crystallography

Gao, S.Pan, M.Zheng, Y.Huang, Y.Zheng, Q.Sun, D.Lu, L.Tan, X.Tan, X.Lan, H.Wang, J.Wang, T.Wang, J.Liu, L.

(2016) J.Am.Chem.Soc. 138: 14497-14502

  • DOI: 10.1021/jacs.6b09545
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Racemic or quasi-racemic crystallography recently emerges as a useful technology for solution of the crystal structures of biomacromolecules. It remains unclear to what extent the biomacromolecules of opposite handedness can differ from each other in ...

    Racemic or quasi-racemic crystallography recently emerges as a useful technology for solution of the crystal structures of biomacromolecules. It remains unclear to what extent the biomacromolecules of opposite handedness can differ from each other in racemic or quasi-racemic crystallography. Here we report a finding that monomeric d-ubiquitin (Ub) has propensity to cocrystallize with different dimers, trimers, and even a tetramer of l-Ub. In these cocrystals the unconnected monomeric d-Ubs can self-assemble to form pseudomirror images of different oligomers of l-Ub. This monomer/oligomer cocrystallization phenomenon expands the concept of racemic crystallography. Using the monomer/oligomer cocrystallization technology we obtained, for the first time the X-ray structures of linear M1-linked tri- and tetra-Ubs and a K11/K63-branched tri-Ub.


    Organizational Affiliation

    Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
D-ubiquitin
B
76Homo sapiensMutation(s): 0 
Gene Names: UBA52 (UBCEP2)
Find proteins for P62987 (Homo sapiens)
Go to Gene View: UBA52
Go to UniProtKB:  P62987
Small Molecules
Modified Residues  17 Unique
IDChainsTypeFormula2D DiagramParent
DIL
Query on DIL
B
D-PEPTIDE LINKINGC6 H13 N O2

--

DNE
Query on DNE
B
D-PEPTIDE LINKINGC6 H13 N O2

--

DPR
Query on DPR
B
D-PEPTIDE LINKINGC5 H9 N O2

--

DLY
Query on DLY
B
D-PEPTIDE LINKINGC6 H14 N2 O2

--

DHI
Query on DHI
B
D-PEPTIDE LINKINGC6 H10 N3 O2

--

DSN
Query on DSN
B
D-PEPTIDE LINKINGC3 H7 N O3

--

DVA
Query on DVA
B
D-PEPTIDE LINKINGC5 H11 N O2

--

DTH
Query on DTH
B
D-PEPTIDE LINKINGC4 H9 N O3

--

DLE
Query on DLE
B
D-PEPTIDE LINKINGC6 H13 N O2

--

DGL
Query on DGL
B
D-PEPTIDE LINKINGC5 H9 N O4

--

DAL
Query on DAL
B
D-PEPTIDE LINKINGC3 H7 N O2

--

DPN
Query on DPN
B
D-PEPTIDE LINKINGC9 H11 N O2

--

DGN
Query on DGN
B
D-PEPTIDE LINKINGC5 H10 N2 O3

--

DAS
Query on DAS
B
D-PEPTIDE LINKINGC4 H7 N O4

--

DSG
Query on DSG
B
D-PEPTIDE LINKINGC4 H8 N2 O3

--

DTY
Query on DTY
B
D-PEPTIDE LINKINGC9 H11 N O3

--

DAR
Query on DAR
B
D-PEPTIDE LINKINGC6 H15 N4 O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.153 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.191 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 24.730α = 98.07
b = 26.380β = 93.85
c = 45.120γ = 106.54
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of ChinaChina2013CB932800

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Database references