3S04
Crystal structure of Escherichia coli type I signal peptidase in complex with an Arylomycin Lipoglycopeptide Antibiotic
- PDB DOI: https://doi.org/10.2210/pdb3S04/pdb
- Classification: HYDROLASE/ANTIBIOTIC
- Organism(s): Escherichia coli K-12, Streptomyces sp.
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2011-05-13 Released: 2011-10-05
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.44 Å
- R-Value Free: 0.265
- R-Value Work: 0.245
- R-Value Observed: 0.246
This is version 1.6 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 |
| Signal peptidase I | 250 | Escherichia coli K-12 | Mutation(s): 0 Gene Names: b2568, JW2552, lepB EC: 3.4.21.89 |  | |
UniProt | |||||
Find proteins for P00803 (Escherichia coli (strain K12)) Explore P00803 Go to UniProtKB: P00803 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00803 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Glyco-Arylomycin | C [auth I], D [auth J] | 6 | Streptomyces sp. | Mutation(s): 0 |  |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 02U Query on 02U | E [auth I], H [auth J] | 14-methylhexadec-9-enoic acid C17 H32 O2 JSOOUDKFWVPPEF-UHFFFAOYSA-N |  | ||
| RAM Query on RAM | F [auth I], G [auth J] | alpha-L-rhamnopyranose C6 H12 O5 SHZGCJCMOBCMKK-HGVZOGFYSA-N |  | ||
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000813 Query on PRD_000813 | C [auth I], D [auth J] | Arylomycin | Lipoglycopeptide / Antibiotic |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.44 Å
- R-Value Free: 0.265
- R-Value Work: 0.245
- R-Value Observed: 0.246
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.01 | α = 90 |
| b = 72.01 | β = 90 |
| c = 262.57 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CrystalClear | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| CrystalClear | data reduction |
| CrystalClear | data scaling |
Entry History
Deposition Data
- Released Date: 2011-10-05 Deposition Author(s): Paetzel, M., Luo, C.
Revision History (Full details and data files)
- Version 1.0: 2011-10-05
Type: Initial release - Version 1.1: 2011-11-02
Changes: Database references - Version 1.2: 2011-11-16
Changes: Database references - Version 1.3: 2012-12-12
Changes: Other - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.5: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary - Version 1.6: 2023-12-06
Changes: Data collection, Derived calculations
