Download MendeleyX-ray crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium.
Osipiuk, J., Gu, M., Peterson, S., Anderson, W.F., Joachimiak, A.To be published.
3GHZ | pdb_00003ghz
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium
- PDB DOI: https://doi.org/10.2210/pdb3GHZ/pdb
- Classification: LYASE
- Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-03-04 Released: 2009-03-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.03 Å
- R-Value Free: 0.205 (Depositor), 0.210 (DCC)
- R-Value Work: 0.166 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.168 (Depositor)
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
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 |
| 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 162 | Salmonella enterica subsp. enterica serovar Typhimurium | Mutation(s): 0 Gene Names: ispF, STM2929 EC: 4.6.1.12 |  | |
UniProt | |||||
Find proteins for Q8ZMF7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZMF7 Go to UniProtKB: Q8ZMF7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8ZMF7 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| POP Query on POP | G [auth B] | PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | D [auth A], I [auth C] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| MG Query on MG | E [auth A], F [auth A], H [auth B], J [auth C] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.03 Å
- R-Value Free: 0.205 (Depositor), 0.210 (DCC)
- R-Value Work: 0.166 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.168 (Depositor)
Diffraction Data: https://doi.org/10.18430/m33ghz
Space Group: I 2 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 143.974 | α = 90 |
| b = 143.974 | β = 90 |
| c = 143.974 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SBC-Collect | data collection |
| MOLREP | phasing |
| HKL-3000 | phasing |
Entry History
Deposition Data
- Released Date: 2009-03-17 Deposition Author(s): Osipiuk, J., Gu, M., Peterson, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Revision History (Full details and data files)
- Version 1.0: 2009-03-17
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
