8XGQ | pdb_00008xgq

The co-crystal structure of LtpM with UDP

PDB DOI: https://doi.org/10.2210/pdb8XGQ/pdb

Classification: TRANSFERASE
Organism(s): Legionella pneumophila subsp. pneumophila
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2023-12-15 Released: 2024-12-18
Deposition Author(s): Wei, T., Xiao, J.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free:
0.301 (Depositor), 0.304 (DCC)
R-Value Work:
0.257 (Depositor), 0.269 (DCC)
R-Value Observed:
0.262 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The co-crystal structure of LtpM with UDP

Wei, T., Xiao, J.

To be published.

Macromolecule Content

Total Structure Weight: 97.68 kDa
Atom Count: 6,111
Modeled Residue Count: 757
Deposited Residue Count: 852
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LtpM1	A [auth B], B [auth A]	426	Legionella pneumophila subsp. pneumophila	Mutation(s): 0 Gene Names: D1H98_02725
UniProt
Find proteins for A0A3A6VV34 (Legionella pneumophila subsp. pneumophila) Explore A0A3A6VV34 Go to UniProtKB: A0A3A6VV34
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3A6VV34
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 A] SDF format, chain C [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth B]	C [auth B], D [auth A]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain C [auth B] Focus chain D [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free: 0.301 (Depositor), 0.304 (DCC)
R-Value Work: 0.257 (Depositor), 0.269 (DCC)
R-Value Observed: 0.262 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.593	α = 109.92
b = 64.925	β = 94.24
c = 84.423	γ = 109.06

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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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-12-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-12-18
Type: Initial release

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.