7MCO | pdb_00007mco

Crystal Structure of Tetur04g02350

PDB DOI: https://doi.org/10.2210/pdb7MCO/pdb

Classification: TRANSFERASE
Organism(s): Tetranychus urticae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-04-02 Released: 2022-04-27
Deposition Author(s): Danehsian, L., Kluza, A., Dermauw, W., Wybouw, N., Van Leeuwen, T., Chruszcz, M.
Funding Organization(s): United States Department of Agriculture (USDA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.203 (Depositor), 0.208 (DCC)
R-Value Work:
0.158 (Depositor), 0.166 (DCC)

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 Tetur04g02350

Danehsian, L., Kluza, A., Dermauw, W., Wybouw, N., Van Leeuwen, T., Chruszcz, M.

To be published.

Macromolecule Content

Total Structure Weight: 106.2 kDa
Atom Count: 7,771
Modeled Residue Count: 854
Deposited Residue Count: 922
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glycosyltransferase 203A2	A, B	461	Tetranychus urticae	Mutation(s): 0 Gene Names: 107359436, UGT203A2
UniProt
Find proteins for T1K1R5 (Tetranychus urticae) Explore T1K1R5 Go to UniProtKB: T1K1R5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	T1K1R5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP (Subject of Investigation/LOI) Query on UDP 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]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.203 (Depositor), 0.208 (DCC)
R-Value Work: 0.158 (Depositor), 0.166 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.189	α = 88.544
b = 66.085	β = 72.78
c = 75.971	γ = 87.401

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-04-27

Deposition Author(s):

Van Leeuwen, T.

Funding Organization	Location	Grant Number
United States Department of Agriculture (USDA)	United States	2020-67014-31179

Revision History (Full details and data files)

Version 1.0: 2022-04-27
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, 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.