3OLN | pdb_00003oln

Crystal structure of the SRA domain of E3 ubiquitin-protein ligase UHRF2

PDB DOI: https://doi.org/10.2210/pdb3OLN/pdb

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

Deposited: 2010-08-26 Released: 2010-10-13
Deposition Author(s): Walker, J.R., Xue, S., Avvakumov, G.V., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.234 (Depositor), 0.217 (DCC)
R-Value Work:
0.184 (Depositor)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3OLN

This is version 1.2 of the entry. See complete history.

Literature

The Set and Ring Associated (SRA) domain of human ubiquitin-like containing PHD and RING finger domains 2 (UHRF2)

Walker, J.R., Xue, S., Avvakumov, G.V., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 51.27 kDa
Atom Count: 2,997
Modeled Residue Count: 366
Deposited Residue Count: 462
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF2	A, B	231	Homo sapiens	Mutation(s): 0 Gene Names: NIRF, RNF107, EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PU4 (Homo sapiens) Explore Q96PU4 Go to UniProtKB: Q96PU4
PHAROS: Q96PU4 GTEx: ENSG00000147854
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96PU4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.234 (Depositor), 0.217 (DCC)
R-Value Work: 0.184 (Depositor)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.528	α = 104.55
b = 46.259	β = 93.87
c = 58.307	γ = 90.08

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-10-13

Deposition Author(s):

Avvakumov, G.V.

Arrowsmith, C.H.

Dhe-Paganon, S.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Refinement description

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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.