7VAA | pdb_00007vaa

Crystal structure of MiCGT(W93V/V124F/ F191A/R282H) in complex with UDPs

PDB DOI: https://doi.org/10.2210/pdb7VAA/pdb

Classification: TRANSFERASE
Organism(s): Mangifera indica
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-08-27 Released: 2022-07-06
Deposition Author(s): Zhong, L., Zhang, Z.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.289 (Depositor), 0.287 (DCC)
R-Value Work:
0.245 (Depositor)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Directed Evolution of a Plant Glycosyltransferase for Chemo- and Regioselective Glycosylation of Pharmaceutically Significant Flavonoids

Wen, Z., Zhang, Z.M., Zhong, L., Fan, J., Li, M., Ma, Y., Zhou, Y., Zhang, W., Guo, B., Chen, B., Wang, J.B.

(2021) ACS Catal 11: 14781-14790

DOI: https://doi.org/10.1021/acscatal.1c04191

Macromolecule Content

Total Structure Weight: 104.9 kDa
Atom Count: 7,036
Modeled Residue Count: 906
Deposited Residue Count: 940
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glycosyltransferase 13	A, B	470	Mangifera indica	Mutation(s): 4 Gene Names: CGT, UGT13 EC: 2.4.1
UniProt
Find proteins for A0A0M4KE44 (Mangifera indica) Explore A0A0M4KE44 Go to UniProtKB: A0A0M4KE44
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0M4KE44
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] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.289 (Depositor), 0.287 (DCC)
R-Value Work: 0.245 (Depositor)
R-Value Observed: 0.250 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.705	α = 90
b = 103.759	β = 90
c = 109.713	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
Coot	model building
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-07-06
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary

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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.