9BIV | pdb_00009biv

Crystal Structure of Ubc13 with a New Active Site Loop Conformation

PDB DOI: https://doi.org/10.2210/pdb9BIV/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-04-24 Released: 2024-05-08
Deposition Author(s): Farraj, R.A., Edwards, R.A., Glover, J.N.M.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.177 (Depositor), 0.178 (DCC)
R-Value Work:
0.144 (Depositor), 0.146 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Ubc13 with a New Active Site Loop Conformation

Farraj, R.A., Edwards, R.A., Glover, J.N.M.

To be published.

Macromolecule Content

Total Structure Weight: 33.54 kDa
Atom Count: 2,735
Modeled Residue Count: 288
Deposited Residue Count: 297
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 variant 2	A	145	Homo sapiens	Mutation(s): 0 Gene Names: UBE2V2, MMS2, UEV2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15819 (Homo sapiens) Explore Q15819 Go to UniProtKB: Q15819
PHAROS: Q15819 GTEx: ENSG00000169139
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15819
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 N	B	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61088
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.177 (Depositor), 0.178 (DCC)
R-Value Work: 0.144 (Depositor), 0.146 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.361	α = 90
b = 42.942	β = 108.37
c = 93.79	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2024-05-08
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.