Download MendeleyCrystal structure of the L,D-transpeptidase (residues 123-326) from Xylanimonas cellulosilytica DSM 15894
Nocek, B., Bigelow, L., Endres, M., Babnigg, G., Joachimiak, A.To be published.
4LPQ
Crystal structure of the L,D-transpeptidase (residues 123-326) from Xylanimonas cellulosilytica DSM 15894
- PDB DOI: 10.2210/pdb4LPQ/pdb
- Classification: TRANSFERASE
- Organism(s): Xylanimonas cellulosilytica DSM 15894
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2013-07-16 Released: 2013-11-13
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.37 Å
- R-Value Free: 0.146
- R-Value Work: 0.122
- R-Value Observed: 0.123
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ErfK/YbiS/YcfS/YnhG family protein | A | 207 | Xylanimonas cellulosilytica DSM 15894 | Mutation(s): 0 Gene Names: Xcel_0604 |  |
UniProt | |||||
Find proteins for D1BWR1 (Xylanimonas cellulosilytica (strain DSM 15894 / CECT 5975 / LMG 20990 / XIL07)) Explore D1BWR1 Go to UniProtKB: D1BWR1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D1BWR1 | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CL Query on CL | B [auth A], C [auth A], D [auth A], E [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | 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: 1.37 Å
- R-Value Free: 0.146
- R-Value Work: 0.122
- R-Value Observed: 0.123
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 62.849 | α = 90 |
| b = 62.849 | β = 90 |
| c = 167.21 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| HKL-3000 | phasing |
| MLPHARE | phasing |
| DM | model building |
| ARP/wARP | model building |
| CCP$ | model building |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| DM | phasing |
| CCP4 | phasing |
Entry History
Deposition Data
- Deposited Date: 2013-07-16
- Released Date: 2013-11-13 Deposition Author(s): Nocek, B., Bigelow, L., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2013-11-13
Type: Initial release
