2XY7
Crystal structure of a salicylic aldehyde base in the pre-insertion site of fragment DNA polymerase I from Bacillus stearothermophilus
- PDB DOI: https://doi.org/10.2210/pdb2XY7/pdb
- NAKB: 2XY7
- Classification: TRANSFERASE/DNA
- Organism(s): Geobacillus stearothermophilus, synthetic construct
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2010-11-15 Released: 2011-07-27
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.05 Å
- R-Value Free: 0.284
- R-Value Work: 0.236
- R-Value Observed: 0.239
wwPDB Validation 3D Report Full Report
This is version 2.1 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA POLYMERASE I | 580 | Geobacillus stearothermophilus | Mutation(s): 1 EC: 2.7.7.7 |  | |
UniProt | |||||
Find proteins for E1C9K5 (Geobacillus stearothermophilus) Explore E1C9K5 Go to UniProtKB: E1C9K5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | E1C9K5 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP)-3' | 10 | synthetic construct |  | ||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5'-D(*SAYP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP)-3' | 11 | synthetic construct |  | ||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | E [auth A], F [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900003 Query on PRD_900003 | D | sucrose | Oligosaccharide / Nutrient |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.05 Å
- R-Value Free: 0.284
- R-Value Work: 0.236
- R-Value Observed: 0.239
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 86.037 | α = 90 |
| b = 94.022 | β = 90 |
| c = 106.711 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2011-07-27 Deposition Author(s): Kaul, C., Mueller, M., Wagner, M., Schneider, S., Carell, T.
Revision History (Full details and data files)
- Version 1.0: 2011-07-27
Type: Initial release - Version 1.1: 2011-10-05
Changes: Database references - Version 1.2: 2012-03-28
Changes: Other - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary - Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary
