6UPU

Crystal structure of the Orientia tsutsugamushi OtDUB in complex with three molecules of ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report



Literature

A Ulp1-like Deubiquitylase from the Human Pathogen Orientia tsutsugamushi with a Novel Domain of Unusually High Ubiquitin Affinity

Berk, J.M.Lim, C.S.Ronau, J.A.Chaudhuri, A.Chen, H.Beckmann, J.Loria, J.P.Xiong, Y.Hochstrasser, M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ULP_PROTEASE domain-containing protein AEIM260Orientia tsutsugamushi str. IkedaMutation(s): 0 
Gene Names: OTT_1962
Find proteins for B3CVM3 (Orientia tsutsugamushi (strain Ikeda))
Explore B3CVM3 
Go to UniProtKB:  B3CVM3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinBCDFGHJKBCDFGHJKLNOP
79Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS:  P0CG48
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.745α = 90
b = 144.074β = 90
c = 143.474γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01-AI116313
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM046904
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM053756

Revision History 

  • Version 1.0: 2020-04-01
    Type: Initial release