6NYS | pdb_00006nys

The crystal structure of CroV588 a novel circular LRR protein structure

PDB DOI: https://doi.org/10.2210/pdb6NYS/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Cafeteria roenbergensis virus
Expression System: Escherichia coli
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: 3.10 Å
R-Value Free:
0.296 (Depositor), 0.310 (DCC)
R-Value Work:
0.261 (Depositor), 0.260 (DCC)
R-Value Observed:
0.263 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 179.15 kDa
Atom Count: 11,520
Modeled Residue Count: 1,358
Deposited Residue Count: 1,362
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
crov588	A [auth B], B [auth A]	681	Cafeteria roenbergensis virus	Mutation(s): 0
UniProt
Find proteins for A0A4D6WFR4 (Cafeteria roenbergensis virus) Explore A0A4D6WFR4 Go to UniProtKB: A0A4D6WFR4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4D6WFR4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TEW Query on TEW Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	C [auth B] D [auth B] E [auth B] F [auth B] G [auth B] C [auth B], D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	6-tungstotellurate(VI) O₂₄ Te W₆ JDLYBIMRCSJRQJ-UHFFFAOYSA-M		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.296 (Depositor), 0.310 (DCC)
R-Value Work: 0.261 (Depositor), 0.260 (DCC)
R-Value Observed: 0.263 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.289	α = 90
b = 171.757	β = 90.12
c = 92.031	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-08-12

Deposition Author(s):

Huyton, T.

Jaiswal, M.

Gorlich, D.

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: Advisory, Data collection, Database references, Refinement description