2RJ2 | pdb_00002rj2

Crystal Structure of the Sugar Recognizing SCF Ubiquitin Ligase at 1.7 Resolution

PDB DOI: https://doi.org/10.2210/pdb2RJ2/pdb

Classification: LIGASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-10-14 Released: 2008-10-14
Deposition Author(s): Vaijayanthimala, S., Velmurugan, D., Mizushima, T., Yamane, T., Yoshida, Y., Tanaka, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.215 (Depositor), 0.211 (DCC)
R-Value Work:
0.185 (Depositor), 0.183 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Sugar Recognizing SCF Ubiquitin Ligase at 1.7 Resolution

Vaijayanthimala, S., Velmurugan, D., Mizushima, T., Yamane, T., Yoshida, Y., Tanaka, K.

To be published.

Macromolecule Content

Total Structure Weight: 21.25 kDa
Atom Count: 1,755
Modeled Residue Count: 185
Deposited Residue Count: 185
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F-box only protein 2	A	185	Mus musculus	Mutation(s): 0 Gene Names: Fbxo2, Fbx2 EC: 6.3.2.19
UniProt & NIH Common Fund Data Resources
Find proteins for Q80UW2 (Mus musculus) Explore Q80UW2 Go to UniProtKB: Q80UW2
IMPC: MGI:2446216
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q80UW2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.215 (Depositor), 0.211 (DCC)
R-Value Work: 0.185 (Depositor), 0.183 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.76	α = 90
b = 61.76	β = 90
c = 115	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-10-14

Deposition Author(s):

Vaijayanthimala, S.

Revision History (Full details and data files)

Version 1.0: 2008-10-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-01-25
Changes: Database references, Derived calculations
Version 1.3: 2023-11-08
Changes: Data collection, 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.