Download MendeleyCrystal Structure of L-Rhamnonate Dehydratase from Salmonella Typhimurium Lt2
Malashkevich, V.N., Sauder, J.M., Dickey, M., Ozyurt, S., Wasserman, S.R., Gerlt, J., Burley, S.K., Almo, S.C.To be published.
2P3Z | pdb_00002p3z
Crystal structure of L-Rhamnonate dehydratase from Salmonella typhimurium
- PDB DOI: https://doi.org/10.2210/pdb2P3Z/pdb
- Classification: LYASE
- Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2007-03-10 Released: 2007-03-20
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.252 (Depositor), 0.250 (DCC)
- R-Value Work: 0.201 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.204 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.7 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 |
| L-rhamnonate dehydratase | 415 | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | Mutation(s): 0 Gene Names: yfaW, STM2291 EC: 4.2.1.90 |  | |
UniProt | |||||
Find proteins for Q8ZNF9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZNF9 Go to UniProtKB: Q8ZNF9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8ZNF9 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NA Query on NA | C [auth A], D [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.252 (Depositor), 0.250 (DCC)
- R-Value Work: 0.201 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.204 (Depositor)
Space Group: F 4 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 272.248 | α = 90 |
| b = 272.248 | β = 90 |
| c = 272.248 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| SHELX | refinement |
| DENZO | data reduction |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2007-03-20 Deposition Author(s): Malashkevich, V.N., Sauder, J.M., Dickey, M., Adams, J.M., Burley, S.K., Wasserman, S.R., Gerlt, J., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2007-03-20
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description - Version 1.4: 2018-11-14
Changes: Data collection, Structure summary - Version 1.5: 2019-07-24
Changes: Data collection, Refinement description - Version 1.6: 2021-02-03
Changes: Database references, Derived calculations, Structure summary - Version 1.7: 2023-08-30
Changes: Data collection, Database references, Refinement description
