7NCY | pdb_00007ncy

Dual specificity phosphatase from Sulfolobales Beppu filamentous virus 3

PDB DOI: https://doi.org/10.2210/pdb7NCY/pdb

Classification: VIRAL PROTEIN
Organism(s): Sulfolobales Beppu filamentous virus 3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-01-29 Released: 2022-03-02
Deposition Author(s): Welin, M., Akutsu, M., Hakansson, M., Al-Karadaghi, S., Jasilionis, A., Nordberg Karlsson, E.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.220 (Depositor), 0.222 (DCC)
R-Value Work:
0.176 (Depositor), 0.178 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 7NCY

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

Literature

Dual specificity phosphatase from Sulfolobales Beppu filamentous virus 3

Welin, M., Akutsu, M., Hakansson, M., Al-Karadaghi, S., Jasilionis, A., Nordberg Karlsson, E.

To be published.

Macromolecule Content

Total Structure Weight: 32.74 kDa
Atom Count: 2,365
Modeled Residue Count: 263
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity phosphatase	A, B	136	Sulfolobales Beppu filamentous virus 3	Mutation(s): 0 Gene Names: SBFV3_gp41
UniProt
Find proteins for A0A3Q8Q3X3 (Sulfolobales Beppu filamentous virus 3) Explore A0A3Q8Q3X3 Go to UniProtKB: A0A3Q8Q3X3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3Q8Q3X3
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.220 (Depositor), 0.222 (DCC)
R-Value Work: 0.176 (Depositor), 0.178 (DCC)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.62	α = 90
b = 59.62	β = 90
c = 167.123	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
SHARP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-02

Deposition Author(s):

Al-Karadaghi, S.

Nordberg Karlsson, E.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	685778

Revision History (Full details and data files)

Version 1.0: 2022-03-02
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Derived calculations, Structure summary

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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.