6LP2 | pdb_00006lp2

Structure of Lpg2148/UBE2N-Ub complex

• PDB DOI: https://doi.org/10.2210/pdb6LP2/pdb

• Classification: TRANSFERASE
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-01-08 Released: 2021-01-13 
• Deposition Author(s): Feng, Y., Wang, Y., Huang, Y., Li, D.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Models: experimental

Literature

Structure of Lpg2148/UBE2N-Ub complex

Feng, Y., Wang, Y., Huang, Y., Li, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 69.89 kDa 
• Atom Count: 4,985 
• Modelled Residue Count: 606 
• Deposited Residue Count: 614 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein lpg2148	A	386	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 1  Gene Names: lpg2148
UniProt
Find proteins for Q5ZTL3 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZTL3  Go to UniProtKB:  Q5ZTL3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B [auth C]	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 N	C [auth D]	152	Homo sapiens	Mutation(s): 0  Gene Names: UBE2N, BLU EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens) Explore P61088  Go to UniProtKB:  P61088
PHAROS:  P61088 GTEx:  ENSG00000177889

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.953	α = 90
b = 71.266	β = 90.74
c = 75.111	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Feng, Y., Wang, Y., Huang, Y., Li, D.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31822012

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description