7WUN | pdb_00007wun

Crystal structure of UBR bof from PRT6 (RSG)

PDB DOI: https://doi.org/10.2210/pdb7WUN/pdb

Classification: LIGASE
Organism(s): Oryza sativa, Oryza sativa Japonica Group
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-08 Released: 2023-02-08
Deposition Author(s): Ho, M.C., Cao, C.C.
Funding Organization(s): Academia Sinica (Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free:
0.186 (Depositor), 0.186 (DCC)
R-Value Work:
0.167 (Depositor), 0.169 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7WUN

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

Literature

Crystal structure of UBR box from PRT6

Ho, M.C., Cao, J.J.

To be published.

Macromolecule Content

Total Structure Weight: 8.44 kDa
Atom Count: 663
Modeled Residue Count: 73
Deposited Residue Count: 75
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-mer peptide	A [auth X]	3	Oryza sativa	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase	B [auth A]	72	Oryza sativa Japonica Group	Mutation(s): 0 Gene Names: Os01g0148000, OSNPB_010148000 EC: 2.3.2.27
UniProt
Find proteins for A0A0P0UY23 (Oryza sativa subsp. japonica) Explore A0A0P0UY23 Go to UniProtKB: A0A0P0UY23
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0P0UY23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.186 (Depositor), 0.186 (DCC)
R-Value Work: 0.167 (Depositor), 0.169 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.803	α = 90
b = 29.803	β = 90
c = 114.755	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	--

Revision History (Full details and data files)

Version 1.0: 2023-02-08
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.