Download MendeleyStructure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation
Gokulan, K., Khare, S., Cerniglia, C.E., Foley, S.L., Varughese, K.I.To be published.
4QRA | pdb_00004qra
Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation
- PDB DOI: https://doi.org/10.2210/pdb4QRA/pdb
- Classification: HYDROLASE
- Organism(s): Mycobacterium tuberculosis H37Rv
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2014-06-30 Released: 2015-12-23
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.29 Å
- R-Value Free: 0.226 (Depositor), 0.230 (DCC)
- R-Value Work: 0.182 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.184 (Depositor)
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) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| L,d-transpeptidase LdtB | 352 | Mycobacterium tuberculosis H37Rv | Mutation(s): 0 Gene Names: ldtB, Rv2518c, RVBD_2518c EC: 2.3.2 |  | |
UniProt | |||||
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y9J2 Go to UniProtKB: I6Y9J2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | I6Y9J2 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CA Query on CA | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.29 Å
- R-Value Free: 0.226 (Depositor), 0.230 (DCC)
- R-Value Work: 0.182 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.184 (Depositor)
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 113.758 | α = 90 |
| b = 88.132 | β = 90.02 |
| c = 90.512 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| MLPHARE | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2015-12-23 Deposition Author(s): Gokulan, K., Varughese, K.I.
Revision History (Full details and data files)
- Version 1.0: 2015-12-23
Type: Initial release - Version 1.1: 2016-08-24
Changes: Structure summary - Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations
