3B4C
T. tengcongensis glmS ribozyme bound to glucosamine-6-phosphate and a substrate RNA with a 2'5'-phosphodiester linkage
- PDB DOI: https://doi.org/10.2210/pdb3B4C/pdb
- NAKB: 3B4C
- Classification: RNA
- Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis
- Mutation(s): No 
- Deposited: 2007-10-23 Released: 2007-12-11 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.262 
- R-Value Work: 0.228 
This is version 1.3 of the entry. See complete history. 
Macromolecules
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
glmS ribozyme substrate with a 2'5'-phosphodiester linkage | 26 | Caldanaerobacter subterraneus subsp. tengcongensis | |||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
glmS ribozyme RNA | 125 | Caldanaerobacter subterraneus subsp. tengcongensis | |||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 3 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 | |||
3AD Query on 3AD | F [auth A] | 3'-DEOXYADENOSINE C10 H13 N5 O3 OFEZSBMBBKLLBJ-BAJZRUMYSA-N | |||
MG Query on MG | D [auth A], E [auth A], G [auth B], H [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.262 
- R-Value Work: 0.228 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 178.3 | α = 90 |
b = 40.4 | β = 90 |
c = 77.5 | γ = 90 |
Software Name | Purpose |
---|---|
CNS | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2007-12-11  Deposition Author(s): Klein, D.J., Ferre-D'Amare, A.R.
Revision History (Full details and data files)
- Version 1.0: 2007-12-11
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.3: 2024-02-21
Changes: Data collection, Database references, Structure summary