7BV3 | pdb_00007bv3

Crystal structure of a ugt transferase from Siraitia grosvenorii in complex with UDP

PDB DOI: https://doi.org/10.2210/pdb7BV3/pdb

Classification: TRANSFERASE
Organism(s): Siraitia grosvenorii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-04-09 Released: 2021-03-03
Deposition Author(s): Li, J., Shan, N., Yang, J.G., Liu, W.D., Sun, Y.X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.196 (Depositor), 0.196 (DCC)
R-Value Work:
0.174 (Depositor), 0.178 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Near-perfect control of the regioselective glucosylation enabled by rational design of glycosyltransferases

Li, J., Qu, G., Shang, N., Chen, P., Men, Y., Liu, W.D., Mei, Z., Sun, Y.X., Sun, Z.

(2021) Green Synth Catal

DOI: https://doi.org/10.1016/j.gresc.2021.01.005

Macromolecule Content

Total Structure Weight: 106.42 kDa
Atom Count: 7,650
Modeled Residue Count: 896
Deposited Residue Count: 966
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A, B	483	Siraitia grosvenorii	Mutation(s): 0 Gene Names: UGT74AC2 EC: 2.4.1
UniProt
Find proteins for A0A346A6C4 (Siraitia grosvenorii) Explore A0A346A6C4 Go to UniProtKB: A0A346A6C4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A346A6C4
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 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]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-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: 1.85 Å
R-Value Free: 0.196 (Depositor), 0.196 (DCC)
R-Value Work: 0.174 (Depositor), 0.178 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 197.52	α = 90
b = 63.71	β = 101.65
c = 93.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-03-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-03-03
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.