6YDR | pdb_00006ydr

Crystal structure of Mengla Virus VP30 C-terminal domain

PDB DOI: https://doi.org/10.2210/pdb6YDR/pdb

Classification: VIRAL PROTEIN
Organism(s): Dianlovirus menglaense
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2020-03-20 Released: 2020-04-01
Deposition Author(s): Tomas Gilabert, O., Ferrero, D.S., Verdaguer, N.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free:
0.155 (Depositor), 0.154 (DCC)
R-Value Work:
0.127 (Depositor), 0.127 (DCC)
R-Value Observed:
0.128 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Mengla Virus VP30 C-terminal domain

Tomas Gilabert, O., Ferrero, D.S., Verdaguer, N.

To be published.

Macromolecule Content

Total Structure Weight: 16.94 kDa
Atom Count: 1,232
Modeled Residue Count: 129
Deposited Residue Count: 152
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Minor nucleoprotein VP30	A	152	Dianlovirus menglaense	Mutation(s): 0 Gene Names: VP30
UniProt
Find proteins for A0A3S8UVN5 (Dianlovirus menglaense) Explore A0A3S8UVN5 Go to UniProtKB: A0A3S8UVN5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3S8UVN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free: 0.155 (Depositor), 0.154 (DCC)
R-Value Work: 0.127 (Depositor), 0.127 (DCC)
R-Value Observed: 0.128 (Depositor)

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.062	α = 90
b = 73.062	β = 90
c = 53.459	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-01

Deposition Author(s):

Tomas Gilabert, O.

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BIO2017-83906-P

Revision History (Full details and data files)

Version 1.0: 2020-04-01
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, 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.