6NYR | pdb_00006nyr

The crystal structure of CroV588 a novel circular LRR protein structure

PDB DOI: https://doi.org/10.2210/pdb6NYR/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Rheavirus
Expression System: Escherichia
Mutation(s): No

Deposited: 2019-02-12 Released: 2020-08-12
Deposition Author(s): Huyton, T., Jaiswal, M., Gorlich, D.
Funding Organization(s): German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free:
0.257 (Depositor), 0.258 (DCC)
R-Value Work:
0.220 (Depositor), 0.222 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of CroV588 a novel circular LRR protein structure

Huyton, T., Jaiswal, M., Gorlich, D.

To be published.

Macromolecule Content

Total Structure Weight: 157.01 kDa
Atom Count: 11,954
Modeled Residue Count: 1,360
Deposited Residue Count: 1,362
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Crov588	A, B	681	Rheavirus	Mutation(s): 0
UniProt
Find proteins for A0A4D6WFR4 (Cafeteria roenbergensis virus) Explore A0A4D6WFR4 Go to UniProtKB: A0A4D6WFR4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4D6WFR4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.257 (Depositor), 0.258 (DCC)
R-Value Work: 0.220 (Depositor), 0.222 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.403	α = 90
b = 172.62	β = 94.79
c = 92.333	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-08-12

Deposition Author(s):

Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	SFB

Revision History (Full details and data files)

Version 1.0: 2020-08-12
Type: Initial release
Version 1.1: 2024-03-13
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.