Download MendeleyCrystal structure of Spr0440 glycoside hydrolase domain, Endo-D from Streptococcus pneumoniae R6
Jiang, Y.-L., Frolet, C., Di-guilmi, A.-M., Zhou, C.-Z., Vernet, T., Chen, Y.-X.To be published.
3GDB
Crystal structure of Spr0440 glycoside hydrolase domain, Endo-D from Streptococcus pneumoniae R6
- PDB DOI: https://doi.org/10.2210/pdb3GDB/pdb
- Classification: HYDROLASE
- Organism(s): Streptococcus pneumoniae R6
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-02-24 Released: 2009-03-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.87 Å
- R-Value Free: 0.204
- R-Value Work: 0.161
- R-Value Observed: 0.164
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 |
| Putative uncharacterized protein spr0440 | 937 | Streptococcus pneumoniae R6 | Mutation(s): 0 Gene Names: spr0440 EC: 3.2.1.96 |  | |
UniProt | |||||
Find proteins for Q8CZ52 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8CZ52 Go to UniProtKB: Q8CZ52 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8CZ52 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PGE Query on PGE | D [auth A] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| ACY Query on ACY | B [auth A], C [auth A] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.87 Å
- R-Value Free: 0.204
- R-Value Work: 0.161
- R-Value Observed: 0.164
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 135.14 | α = 90 |
| b = 59.06 | β = 110.27 |
| c = 94.89 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MAR345dtb | data collection |
| SOLVE | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2009-03-17 Deposition Author(s): Jiang, Y.-L., Frolet, C., Di-guilmi, A.-M., Zhou, C.-Z., Vernet, T., Chen, Y.-X.
Revision History (Full details and data files)
- Version 1.0: 2009-03-17
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations
