Download MendeleyCrystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1.
Hong, M.K., Kim, J.K., Jung, J.H., Jung, J.W., Choi, J.Y., Kang, L.W.To be published.
3DKU | pdb_00003dku
Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1
- PDB DOI: https://doi.org/10.2210/pdb3DKU/pdb
- Classification: HYDROLASE
- Organism(s): Escherichia coli APEC O1
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-06-26 Released: 2009-06-30
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.69 Å
- R-Value Free: 0.270 (Depositor), 0.270 (DCC)
- R-Value Work: 0.193 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.196 (Depositor)
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
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 |
| Putative phosphohydrolase | 153 | Escherichia coli APEC O1 | Mutation(s): 0 EC: 3.6.1 |  | |
UniProt | |||||
Find proteins for A1AA28 (Escherichia coli O1:K1 / APEC) Explore A1AA28 Go to UniProtKB: A1AA28 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1AA28 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.69 Å
- R-Value Free: 0.270 (Depositor), 0.270 (DCC)
- R-Value Work: 0.193 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.196 (Depositor)
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 68.96 | α = 90 |
| b = 70.521 | β = 103.3 |
| c = 145.031 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2009-06-30 Deposition Author(s): Hong, M.K., Kim, J.K., Jung, J.H., Jung, J.W., Choi, J.Y., Kang, L.W.
Revision History (Full details and data files)
- Version 1.0: 2009-06-30
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-10-25
Changes: Author supporting evidence - Version 1.3: 2019-12-25
Changes: Derived calculations - Version 1.4: 2023-08-30
Changes: Data collection, Database references, Refinement description
