4IP3

Complex structure of OspI and Ubc13

PDB DOI: https://doi.org/10.2210/pdb4IP3/pdb

Classification: UNKNOWN FUNCTION/Ligase
Organism(s): Shigella flexneri, Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-01-09 Released: 2013-03-20
Deposition Author(s): Fu, P., Jin, M., Zhang, X., Xu, L., Xia, Z., Zhu, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.248
R-Value Work: 0.210
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure Analysis of Ubc13 Inactivation

Fu, P., Jin, M., Zhang, X., Xu, L., Xia, Z., Zhu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 42.81 kDa
Atom Count: 2,837
Modelled Residue Count: 343
Deposited Residue Count: 386
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF169b	A	214	Shigella flexneri	Mutation(s): 1 Gene Names: CP0209, ORF169b, OspI
UniProt
Find proteins for Q8VSD5 (Shigella flexneri) Explore Q8VSD5 Go to UniProtKB: Q8VSD5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8VSD5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 N	B	172	Homo sapiens	Mutation(s): 0 Gene Names: BLU, Ubc13, UBE2N EC: 6.3.2.19
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61088
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.248
R-Value Work: 0.210
R-Value Observed: 0.214
Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.06	α = 90
b = 119.06	β = 90
c = 69.735	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-03-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-03-20
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references

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 R01GM133198.