Download MendeleyCrystal structure of a putative agmatinase from Clostridium difficile
Palani, K., Burley, S.K., Swaminathan, S.To be published.
3LHL
Crystal structure of a putative agmatinase from Clostridium difficile
- PDB DOI: https://doi.org/10.2210/pdb3LHL/pdb
- Classification: HYDROLASE
- Organism(s): Clostridioides difficile 630
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2010-01-22 Released: 2010-02-23
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.238
- R-Value Work: 0.193
- R-Value Observed: 0.193
wwPDB Validation 3D Report Full Report
This is version 1.3 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 |
| Putative agmatinase | 287 | Clostridioides difficile 630 | Mutation(s): 0 Gene Names: CD0891, speB |  | |
UniProt | |||||
Find proteins for Q18A84 (Clostridioides difficile (strain 630)) Explore Q18A84 Go to UniProtKB: Q18A84 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q18A84 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MPD Query on MPD | H [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| PO4 Query on PO4 | F [auth A], G [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| MN Query on MN | B [auth A], C [auth A], D [auth A], E [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| 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: 2.30 Å
- R-Value Free: 0.238
- R-Value Work: 0.193
- R-Value Observed: 0.193
- Space Group: P 63 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 77.35 | α = 90 |
| b = 77.35 | β = 90 |
| c = 166.118 | γ = 120 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| CBASS | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| SHELXD | phasing |
| SHARP | phasing |
| ARP/wARP | model building |
Entry History
Deposition Data
- Released Date: 2010-02-23 Deposition Author(s): Palani, K., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2010-02-23
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2011-11-16
Changes: Atomic model - Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
