Download MendeleyThe crystal structure of thiol:disulfide interchange protein DsbC from Yersinia pestis CO92
Tan, K., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A.To be published.
4NPB
The crystal structure of thiol:disulfide interchange protein DsbC from Yersinia pestis CO92
- PDB DOI: 10.2210/pdb4NPB/pdb
- Classification: ISOMERASE
- Organism(s): Yersinia pestis CO92
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2013-11-21 Released: 2013-12-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.235
- R-Value Work: 0.192
- R-Value Observed: 0.194
wwPDB Validation 3D Report Full Report
This is version 2.0 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 |
| Protein disulfide isomerase II | A, B | 220 | Yersinia pestis CO92 | Mutation(s): 0 Gene Names: dsbC, y3275, Yersinia pestis, YPO0891, YP_3587 |  |
UniProt | |||||
Find proteins for A0A5P8YD62 (Yersinia pestis) Explore A0A5P8YD62 Go to UniProtKB: A0A5P8YD62 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A5P8YD62 | ||||
Protein Feature ViewExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Chain Length | 2D Diagram | Glycosylation | 3D Interactions |
| beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose | C | 2 |  | N/A | Oligosaccharides Interaction |
Glycosylation Resources | |||||
GlyTouCan: G05551OP GlyCosmos: G05551OP | |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PO4 Query on PO4 | D [auth A], E [auth B] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900003 Query on PRD_900003 | C | sucrose | Oligosaccharide / Nutrient |  | Ligand Interaction |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.235
- R-Value Work: 0.192
- R-Value Observed: 0.194
- Space Group: P 21 21 2
- Diffraction Data DOI: 10.18430/M34NPB Protein Diffraction
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 90.894 | α = 90 |
| b = 141.335 | β = 90 |
| c = 41.153 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| SHELXD | phasing |
| MLPHARE | phasing |
| DM | model building |
| ARP | model building |
| WARP | model building |
| HKL-3000 | phasing |
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| DM | phasing |
Entry History
Deposition Data
- Deposited Date: 2013-11-21
- Released Date: 2013-12-25 Deposition Author(s): Tan, K., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Revision History (Full details and data files)
- Version 1.0: 2013-12-25
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
