2Z75
T. tengcongensis glmS ribozyme bound to glucosamine-6-phosphate
- PDB DOI: https://doi.org/10.2210/pdb2Z75/pdb
- NAKB: 2Z75
- Classification: DNA, RNA
- Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis MB4
- Mutation(s): No
- Deposited: 2007-08-15 Released: 2007-09-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.239
- R-Value Work: 0.226
This is version 1.4 of the entry. See complete history.
Macromolecules
Find similar nucleic acids by: 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| glmS ribozyme substrate RNA | 27 | Caldanaerobacter subterraneus subsp. tengcongensis MB4 |  | ||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| glmS ribozyme RNA | 125 | Caldanaerobacter subterraneus subsp. tengcongensis MB4 |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GLP Query on GLP | C [auth A] | 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose C6 H14 N O8 P XHMJOUIAFHJHBW-UKFBFLRUSA-N |  | ||
| MG Query on MG | D [auth B] E [auth B] F [auth B] G [auth B] H [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.239
- R-Value Work: 0.226
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 180.935 | α = 90 |
| b = 39.942 | β = 90 |
| c = 70.435 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2007-09-04 Deposition Author(s): Klein, D.J., Wilkinson, S.R., Been, M.D., Ferre-D'Amare, A.R.
Revision History (Full details and data files)
- Version 1.0: 2007-09-04
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2018-04-18
Changes: Data collection, Database references, Source and taxonomy - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary - Version 1.4: 2024-03-13
Changes: Data collection, Database references, Structure summary
