6FBT
The X-ray Structure of Lytic Transglycosylase Slt from Pseudomonas aeruginosa in complex with the reaction product NAG-anhNAMpentapeptide
- PDB DOI: https://doi.org/10.2210/pdb6FBT/pdb
- Classification: LYASE
- Organism(s): Pseudomonas aeruginosa
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2017-12-19 Released: 2018-04-18 
- Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.239 
- R-Value Work: 0.180 
- R-Value Observed: 0.183 
This is version 3.1 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 |
Probable soluble lytic transglycosylase | 610 | Pseudomonas aeruginosa | Mutation(s): 0  Gene Names: PA3020 | ||
UniProt | |||||
Find proteins for Q9HZI6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HZI6  Go to UniProtKB:  Q9HZI6 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9HZI6 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
NAG-anhNAMpentapeptide | B [auth E] | 5 | Pseudomonas aeruginosa | Mutation(s): 0  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
AH0 Query on AH0 | I [auth E] | 2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID C11 H17 N O7 ZFEGYUMHFZOYIY-YVNCZSHWSA-N | |||
NAG Query on NAG | H [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
PO4 Query on PO4 | C [auth A], D [auth A], E [auth A], F [auth A], G [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
API Query on API | B [auth E] | L-PEPTIDE LINKING | C7 H14 N2 O4 | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.239 
- R-Value Work: 0.180 
- R-Value Observed: 0.183 
- Space Group: P 63
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 165.526 | α = 90 |
b = 165.526 | β = 90 |
c = 54.733 | γ = 120 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-04-18  Deposition Author(s): Batuecas, M.T., Dominguez-Gil, T., Hermoso, J.A.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) | United States | AI104987 |
Revision History (Full details and data files)
- Version 1.0: 2018-04-18
Type: Initial release - Version 1.1: 2018-05-02
Changes: Data collection, Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2022-03-30
Changes: Author supporting evidence, Database references, Structure summary - Version 2.0: 2022-12-21
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary - Version 3.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Derived calculations - Version 3.1: 2024-01-31
Changes: Refinement description