Download Mendeleycrystal structure of xanthosine phosphorylase bound with xanthine from Yersinia pseudotuberculosis
Kim, J., Ramagopal, U.A., Almo, S.C.To be published.
3ODG
crystal structure of xanthosine phosphorylase bound with xanthine from Yersinia pseudotuberculosis
- PDB DOI: https://doi.org/10.2210/pdb3ODG/pdb
- Classification: TRANSFERASE
- Organism(s): Yersinia pseudotuberculosis
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2010-08-11 Released: 2010-08-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.64 Å
- R-Value Free: 0.187
- R-Value Work: 0.155
- R-Value Observed: 0.157
Starting Model: experimental
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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 |
| Xanthosine phosphorylase | 287 | Yersinia pseudotuberculosis | Mutation(s): 0 Gene Names: pndA, xapA, YPTB1201 EC: 2.4.2 (PDB Primary Data), 2.4.2.1 (UniProt) |  | |
UniProt | |||||
Find proteins for Q66D48 (Yersinia pseudotuberculosis serotype I (strain IP32953)) Explore Q66D48 Go to UniProtKB: Q66D48 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q66D48 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| XAN Query on XAN | B [auth A] | XANTHINE C5 H4 N4 O2 LRFVTYWOQMYALW-UHFFFAOYSA-N |  | ||
| CL Query on CL | C [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.64 Å
- R-Value Free: 0.187
- R-Value Work: 0.155
- R-Value Observed: 0.157
- Space Group: P 63
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 96.47 | α = 90 |
| b = 96.47 | β = 90 |
| c = 48.906 | γ = 120 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| MOLREP | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2010-08-25 Deposition Author(s): Kim, J., Ramagopal, U.A., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2010-08-25
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2021-02-10
Changes: Derived calculations, Structure summary - Version 1.3: 2023-09-06
Changes: Data collection, Database references, Refinement description
