Download MendeleyCrystal structure of a putative glycyl-glycine endopeptidase lytM (RUMGNA_02482) from Ruminococcus gnavus ATCC 29149 at 1.60 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3NYY
Crystal structure of a putative glycyl-glycine endopeptidase lytM (RUMGNA_02482) from Ruminococcus gnavus ATCC 29149 at 1.60 A resolution
- DOI: 10.2210/pdb3NYY/pdb
- Classification: HYDROLASE
- Organism(s): [Ruminococcus] gnavus ATCC 29149
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2010-07-15 Released: 2010-09-15
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.175
- R-Value Work: 0.149
- R-Value Observed: 0.150
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Putative glycyl-glycine endopeptidase lytM | A | 252 | [Ruminococcus] gnavus ATCC 29149 | Mutation(s): 0 Gene Names: RUMGNA_02482 |  |
Find proteins for A7B4J8 (Ruminococcus gnavus (strain ATCC 29149 / VPI C7-9)) Explore A7B4J8 Go to UniProtKB: A7B4J8 | |||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 2PE Query on 2PE | B [auth A], C [auth A], D [auth A] | NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N |  | Ligand Interaction | |
| SO4 Query on SO4 | E [auth A], F [auth A], G [auth A], H [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.175
- R-Value Work: 0.149
- R-Value Observed: 0.150
- Space Group: C 1 2 1
- Diffraction Data DOI: 10.18430/M33NYY Protein Diffraction
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 91.336 | α = 90 |
| b = 61.572 | β = 108.5 |
| c = 52.804 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SHELX | phasing |
| REFMAC | refinement |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Deposited Date: 2010-07-15
- Released Date: 2010-09-15 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2010-09-15
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2011-07-20
Changes: Structure summary
