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), 0.287 (DCC)
R-Value Work:
0.223 (Depositor)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.271 (Depositor), 0.287 (DCC)
R-Value Work: 0.223 (Depositor)
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

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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

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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.