7D6M | pdb_00007d6m

Crystal structure of tick-borne encephalitis virus methyltransferase

PDB DOI: https://doi.org/10.2210/pdb7D6M/pdb

Classification: TRANSFERASE
Organism(s): Tick-borne encephalitis virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-10-01 Released: 2020-12-23
Deposition Author(s): Yang, J., Jing, X., Gong, P.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.271 (Depositor), 0.270 (DCC)
R-Value Work:
0.223 (Depositor), 0.220 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of tick-borne encephalitis virus

Yang, J., Jing, X., Zhang, B., Zheng, Z., Gong, P.

(2020) Nucleic Acids Res

Macromolecule Content

Total Structure Weight: 61.36 kDa
Atom Count: 4,220
Modeled Residue Count: 520
Deposited Residue Count: 538
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tick-borne encephalitis virus methyltransferase	A, B	269	Tick-borne encephalitis virus	Mutation(s): 0 Gene Names: NS5
UniProt
Find proteins for A0A0E3UPZ3 (Tick-borne encephalitis virus) Explore A0A0E3UPZ3 Go to UniProtKB: A0A0E3UPZ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0E3UPZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM (Subject of Investigation/LOI) Query on SAM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.271 (Depositor), 0.270 (DCC)
R-Value Work: 0.223 (Depositor), 0.220 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.027	α = 79.66
b = 49.468	β = 82.78
c = 85.274	γ = 77.07

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XSCALE	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-12-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2018YFA0507200

Revision History (Full details and data files)

Version 1.0: 2020-12-23
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

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.