6K89 | pdb_00006k89

The closed state of RGLG1 VWA domain

PDB DOI: https://doi.org/10.2210/pdb6K89/pdb

Classification: TRANSFERASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-06-11 Released: 2020-06-24
Deposition Author(s): Wang, Q., Wu, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.231 (Depositor), 0.237 (DCC)
R-Value Work:
0.188 (Depositor), 0.195 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6K89

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

Literature

The closed state of RGLG1 VWA domain

Wang, Q., Wu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 33.21 kDa
Atom Count: 2,428
Modeled Residue Count: 282
Deposited Residue Count: 301
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RGLG1	A [auth B]	301	Arabidopsis thaliana	Mutation(s): 0 Gene Names: RGLG1, At3g01650, F4P13.19 EC: 2.3.2.27
UniProt
Find proteins for Q9SS90 (Arabidopsis thaliana) Explore Q9SS90 Go to UniProtKB: Q9SS90
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SS90
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B Interactions & Density Focus chain B
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.231 (Depositor), 0.237 (DCC)
R-Value Work: 0.188 (Depositor), 0.195 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.619	α = 90
b = 72.935	β = 90
c = 80.077	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-06-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-06-24
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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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.