7CYW | pdb_00007cyw

Crystal structure of a flavonoid C-glucosyltrasferase from Fagopyrum esculentum (FeCGTa) complexed with BrUTP

PDB DOI: https://doi.org/10.2210/pdb7CYW/pdb

Classification: TRANSFERASE
Organism(s): Fagopyrum esculentum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-09-04 Released: 2020-09-23
Deposition Author(s): Koyanagi, Y., Taguchi, G., Arai, R.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.237 (Depositor), 0.241 (DCC)
R-Value Work:
0.201 (Depositor), 0.211 (DCC)
R-Value Observed:
0.203 (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 a flavonoid C-glucosyltrasferase from Fagopyrum esculentum

Koyanagi, Y., Arai, R., Taguchi, G.

To be published.

Macromolecule Content

Total Structure Weight: 49.57 kDa
Atom Count: 3,654
Modeled Residue Count: 428
Deposited Residue Count: 443
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glycosyltransferase 708C1	A	443	Fagopyrum esculentum	Mutation(s): 0 Gene Names: UGT708C1, CGTa EC: 2.4.1 (PDB Primary Data), 2.4.1.360 (UniProt)
UniProt
Find proteins for A0A0A1HA03 (Fagopyrum esculentum) Explore A0A0A1HA03 Go to UniProtKB: A0A0A1HA03
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0A1HA03
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BUP (Subject of Investigation/LOI) Query on BUP 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]	5-bromouridine 5'-(tetrahydrogen triphosphate) C₉ H₁₄ Br N₂ O₁₅ P₃ IWFHOSULCAJGRM-UAKXSSHOSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.237 (Depositor), 0.241 (DCC)
R-Value Work: 0.201 (Depositor), 0.211 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.565	α = 90
b = 76.01	β = 90
c = 93.194	γ = 90

Software Package:

Software Name	Purpose
DENZO	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MR-Rosetta	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-09-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP26450120
Japan Society for the Promotion of Science (JSPS)	Japan	JP20K05825
Japan Society for the Promotion of Science (JSPS)	Japan	JP24780097
Japan Society for the Promotion of Science (JSPS)	Japan	JP16K05841

Revision History (Full details and data files)

Version 1.0: 2020-09-23
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.