3V8V
Crystal structure of bifunctional methyltransferase YcbY (RlmLK) from Escherichia coli, SAM binding
- PDB DOI: https://doi.org/10.2210/pdb3V8V/pdb
- Classification: TRANSFERASE
- Organism(s): Escherichia coli K-12
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2011-12-23 Released: 2012-02-29 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.247 
- R-Value Work: 0.182 
- R-Value Observed: 0.185 
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 |
Ribosomal RNA large subunit methyltransferase L | 702 | Escherichia coli K-12 | Mutation(s): 0  Gene Names: rlmL EC: 2.1.1.173 | ||
UniProt | |||||
Find proteins for P75864 (Escherichia coli (strain K12)) Explore P75864  Go to UniProtKB:  P75864 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P75864 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SAM Query on SAM | E [auth A], F [auth A], G [auth B], H [auth B] | S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900045 Query on PRD_900045 | C, D | octanoyl-sucrose, esterificated at fructose C6 | Oligosaccharide / Substrate analog |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.247 
- R-Value Work: 0.182 
- R-Value Observed: 0.185 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 73.724 | α = 90 |
b = 140.586 | β = 101.88 |
c = 102.097 | γ = 90 |
Software Name | Purpose |
---|---|
MAR345dtb | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2012-02-29  Deposition Author(s): Su, X.D., Wang, K.T.
Revision History (Full details and data files)
- Version 1.0: 2012-02-29
Type: Initial release - Version 1.1: 2013-06-26
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary