Download MendeleyPutative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Uridine
Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.To be published.
3IVD
Putative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Uridine
- PDB DOI: https://doi.org/10.2210/pdb3IVD/pdb
- Classification: HYDROLASE
- Organism(s): Escherichia coli O6
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2009-08-31 Released: 2009-09-29
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 ?
- R-Value Free: 0.210
- R-Value Work: 0.167
- R-Value Observed: 0.169
This is version 1.4 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 |
| Nucleotidase | 509 | Escherichia coli O6 | Mutation(s): 0 Gene Names: c4898 |  | |
UniProt | |||||
Find proteins for A0A0H2VD83 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) Explore A0A0H2VD83 Go to UniProtKB: A0A0H2VD83 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A0H2VD83 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| URI Query on URI | E [auth A], I [auth B] | URIDINE C9 H12 N2 O6 DRTQHJPVMGBUCF-XVFCMESISA-N |  | ||
| FE Query on FE | C [auth A], G [auth B] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |  | ||
| MN Query on MN | D [auth A], H [auth B] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| CL Query on CL | F [auth A], J [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| 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 |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 ?
- R-Value Free: 0.210
- R-Value Work: 0.167
- R-Value Observed: 0.169
- Space Group: P 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 47.597 | ¦Á = 74.04 |
| b = 67.281 | ¦Â = 77.55 |
| c = 86.417 | ¦Ă = 83.76 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| CBASS | data collection |
| HKL-2000 | data reduction |
| SHELXD | phasing |
| SHELXE | model building |
| CCP4 | phasing |
Entry History
Deposition Data
- Released Date: 2009-09-29 Deposition Author(s): Ramagopal, U.A., Toro, R., 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: 2009-09-29
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary - Version 1.4: 2024-11-06
Changes: Data collection, Database references, Structure summary
