6K8A | pdb_00006k8a

RGLG1 VWA domain with MIDAS is occupied by water

PDB DOI: https://doi.org/10.2210/pdb6K8A/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: 2.40 Å
R-Value Free:
0.211 (Depositor), 0.220 (DCC)
R-Value Work:
0.177 (Depositor), 0.186 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

RGLG1 VWA domain with MIDAS is occupied by water

Wang, Q., Wu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 66.57 kDa
Atom Count: 4,515
Modeled Residue Count: 560
Deposited Residue Count: 602
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, 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	C [auth A] D [auth A] E [auth A] F [auth B] G [auth B] C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.211 (Depositor), 0.220 (DCC)
R-Value Work: 0.177 (Depositor), 0.186 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.28	α = 90
b = 136.28	β = 90
c = 55.37	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHENIX	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, Derived calculations

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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.