Download MendeleyCrystal structure of putative lipoprotein from Peptoclostridium difficile 630 (fragment)
Michalska, K., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)To be published.
4YCS | pdb_00004ycs
4YCS | pdb_00004ycs
Crystal structure of putative lipoprotein from Peptoclostridium difficile 630 (fragment)
- PDB DOI: https://doi.org/10.2210/pdb4YCS/pdb
- Classification: HYDROLASE
- Organism(s): Clostridioides difficile 630
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2015-02-20 Released: 2015-03-18
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.98 Å
- R-Value Free: 0.226 (Depositor), 0.236 (DCC)
- R-Value Work: 0.180 (Depositor), 0.188 (DCC)
- R-Value Observed: 0.181 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecule Content
- Total Structure Weight: 85.79 kDa
- Atom Count: 6,108
- Modeled Residue Count: 734
- Deposited Residue Count: 768
- Unique protein chains: 1
Macromolecules
Find similar proteins by:
| 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Uncharacterized protein | 128 | Clostridioides difficile 630 | Mutation(s): 0 Gene Names: BG47_10265 |  | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q189B5 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Download:Ideal Coordinates CCD File | G [auth A], H [auth C], K [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ACT Download:Ideal Coordinates CCD File | I [auth D] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| NA Download:Ideal Coordinates CCD File | J [auth D] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B, C, D, E A, B, C, D, E, F | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.98 Å
- R-Value Free: 0.226 (Depositor), 0.236 (DCC)
- R-Value Work: 0.180 (Depositor), 0.188 (DCC)
- R-Value Observed: 0.181 (Depositor)
Diffraction Data:
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 37.755 | α = 90 |
| b = 119.501 | β = 90 |
| c = 185.912 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| Auto-Rickshaw | phasing |
Entry History
& Funding InformationDeposition Data
- Released Date: 2015-03-18 Deposition Author(s): Michalska, K., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM094585 |
Revision History (Full details and data files)
- Version 1.0: 2015-03-18
Type: Initial release - Version 1.1: 2017-09-27
Changes: Author supporting evidence, Derived calculations, Source and taxonomy - Version 1.2: 2019-12-25
Changes: Author supporting evidence - Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary
