6I0N

Crystal structure of RlpA SPOR domain from Pseudomonas aeruginosa in complex with denuded glycan ended in anhNAM

PDB DOI: https://doi.org/10.2210/pdb6I0N/pdb

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

Deposited: 2018-10-26 Released: 2019-11-13
Deposition Author(s): Alcorlo, M., Hermoso, J.A.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.184
R-Value Work: 0.156
R-Value Observed: 0.158

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 9.15 kDa
Atom Count: 777
Modelled Residue Count: 77
Deposited Residue Count: 77
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endolytic peptidoglycan transglycosylase RlpA	A	77	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: rlpA, PAMH19_1027 EC: 4.2.2
UniProt
Find proteins for Q9X6V6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9X6V6 Go to UniProtKB: Q9X6V6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X6V6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G03158KG GlyCosmos: G03158KG

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AH0 (Subject of Investigation/LOI) Query on AH0 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID C₁₁ H₁₇ N O₇ ZFEGYUMHFZOYIY-YVNCZSHWSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.184
R-Value Work: 0.156
R-Value Observed: 0.158
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.133	α = 90
b = 68.424	β = 90
c = 38.863	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-11-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2014-59389-P and BFU2017-90030-P to JAH

Revision History (Full details and data files)

Version 1.0: 2019-11-13
Type: Initial release
Version 1.1: 2020-05-27
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.