Download MendeleyPutative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Cytidine
Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.To be published.
3IVE
Putative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Cytidine
- PDB DOI: https://doi.org/10.2210/pdb3IVE/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: 1.70 Å
- R-Value Free: 0.190
- R-Value Work: 0.165
- R-Value Observed: 0.167
Starting Model: experimental
View more details
This is version 1.6 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 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CTN Query on CTN | D [auth A] | 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE C9 H13 N3 O5 UHDGCWIWMRVCDJ-XVFCMESISA-N |  | ||
| SO4 Query on SO4 | E [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| FE Query on FE | C [auth A] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |  | ||
| MN Query on MN | B [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| CL Query on CL | F [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.190
- R-Value Work: 0.165
- R-Value Observed: 0.167
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 156.261 | α = 90 |
| b = 77.453 | β = 103.83 |
| c = 47.518 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| CBASS | data collection |
| HKL-2000 | data reduction |
| MOLREP | 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: 2023-09-06
Changes: Data collection, Database references, Refinement description - Version 1.5: 2023-11-22
Changes: Data collection - Version 1.6: 2024-10-09
Changes: Structure summary
