7XGX | pdb_00007xgx

Glucosyltransferase

PDB DOI: https://doi.org/10.2210/pdb7XGX/pdb

Classification: TRANSFERASE
Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-04-07 Released: 2023-04-12
Deposition Author(s): Chen, T.T., Ouyang, S.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.265 (Depositor), 0.258 (DCC)
R-Value Work:
0.215 (Depositor), 0.227 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural Basis for the Action Mechanism of Legionella Glycosyltransferase.

Chen, T.T., Zheng, S.R., Tian, L., Lv, S.L., Zhong, W.H., Li, X.L., Zhang, D.D., Zheng, X.X., Ouyang, S.Y.

(2023) Small Struct

DOI: https://doi.org/10.1002/sstr.202200336

Macromolecule Content

Total Structure Weight: 148.8 kDa
Atom Count: 9,667
Modeled Residue Count: 1,198
Deposited Residue Count: 1,310
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lgt2	A, B	655	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0 Gene Names: C3927_14430
UniProt
Find proteins for Q5ZRL9 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZRL9 Go to UniProtKB: Q5ZRL9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZRL9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UPG (Subject of Investigation/LOI) Query on UPG 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-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-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: 2.39 Å
R-Value Free: 0.265 (Depositor), 0.258 (DCC)
R-Value Work: 0.215 (Depositor), 0.227 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.055	α = 90
b = 75.863	β = 90.24
c = 126.644	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
autoPROC	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-04-12

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2023-04-12
Type: Initial release
Version 1.1: 2023-09-06
Changes: Data collection, Database references
Version 1.2: 2023-09-13
Changes: Source and taxonomy
Version 1.3: 2023-11-29
Changes: 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.