1YLJ
Atomic resolution structure of CTX-M-9 beta-lactamase
- PDB DOI: https://doi.org/10.2210/pdb1YLJ/pdb
- Classification: HYDROLASE
- Organism(s): Escherichia coli
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No 
- Deposited: 2005-01-19 Released: 2005-04-19 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 0.98 Å
- R-Value Free: 0.129 
- R-Value Work: 0.108 
- R-Value Observed: 0.108 
wwPDB Validation   3D Report Full Report
This is version 2.2 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 |
beta-lactamase CTX-M-9a | 263 | Escherichia coli | Mutation(s): 0  Gene Names: CTX-M EC: 3.5.2.6 | ||
UniProt | |||||
Find proteins for Q9L5C8 (Escherichia coli) Explore Q9L5C8  Go to UniProtKB:  Q9L5C8 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9L5C8 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SO4 Query on SO4 | C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900003 Query on PRD_900003 | B | sucrose | Oligosaccharide / Nutrient |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 0.98 Å
- R-Value Free: 0.129 
- R-Value Work: 0.108 
- R-Value Observed: 0.108 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 41.388 | α = 90 |
b = 62.236 | β = 90 |
c = 85.746 | γ = 90 |
Software Name | Purpose |
---|---|
SHELX | model building |
SHELXL-97 | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
SHELX | phasing |
Entry History 
Deposition Data
- Released Date: 2005-04-19  Deposition Author(s): Chen, Y., Delmas, J., Sirot, J., Shoichet, B., Bonnet, R.
Revision History (Full details and data files)
- Version 1.0: 2005-04-19
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2024-02-14
Changes: Data collection, Database references, Structure summary - Version 2.2: 2024-04-03
Changes: Refinement description