7QVD | pdb_00007qvd

X-ray structure of the lytic transglycosylase SltB2 from Pseudomonas aeruginosa

PDB DOI: https://doi.org/10.2210/pdb7QVD/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-01-21 Released: 2023-08-16
Deposition Author(s): Batuecas, M.T., Miguel-Ruano, V., Hermoso, J.A.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.195 (Depositor), 0.210 (DCC)
R-Value Work:
0.164 (Depositor), 0.170 (DCC)

wwPDB Validation 3D Report Full Report

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

Literature

X-ray structure of SltB2 from Pseudomonas aeruginosa

Batuecas, M.T., Miguel-Ruano, V., Hermoso, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 40.93 kDa
Atom Count: 3,309
Modeled Residue Count: 380
Deposited Residue Count: 380
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lytic murein transglycosylase	A [auth AAA]	380	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: IPC1339_08125, IPC1598_14895
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth AAA] Interactions & Density Focus chain B [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.195 (Depositor), 0.210 (DCC)
R-Value Work: 0.164 (Depositor), 0.170 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.966	α = 90
b = 42.395	β = 95.646
c = 93.579	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-16

Deposition Author(s):

Miguel-Ruano, V.

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PRE2018-085033

Revision History (Full details and data files)

Version 1.0: 2023-08-16
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary

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.