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
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8XGQ

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

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.