6I09
Crystal structure of RlpA SPOR domain from Pseudomonas aeruginosa in complex with denuded glycan obtained by soaking
- PDB DOI: https://doi.org/10.2210/pdb6I09/pdb
- Classification: CELL CYCLE
- Organism(s): Pseudomonas aeruginosa
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2018-10-25 Released: 2019-11-13 
- Funding Organization(s): Spanish Ministry of Economy and Competitiveness
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.48 Å
- R-Value Free: 0.199 
- R-Value Work: 0.169 
- R-Value Observed: 0.170 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Endolytic peptidoglycan transglycosylase RlpA | 78 | 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 AnnotationsExpand | |||||
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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-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside | B | 4 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G12322WX GlyCosmos:  G12322WX |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.48 Å
- R-Value Free: 0.199 
- R-Value Work: 0.169 
- R-Value Observed: 0.170 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 67.433 | α = 90 |
b = 68.151 | β = 90 |
c = 38.994 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-11-13  Deposition Author(s): Alcorlo, M., Hermoso, J.A.
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