4B9N
Structure of the high fidelity DNA polymerase I correctly bypassing the oxidative formamidopyrimidine-dA DNA lesion.
- PDB DOI: https://doi.org/10.2210/pdb4B9N/pdb
- NAKB: 4B9N
- Classification: TRANSFERASE/DNA
- Organism(s): Geobacillus stearothermophilus
- Expression System: Escherichia coli BL21
- Mutation(s): No 
- Deposited: 2012-09-05 Released: 2013-04-17 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.217 
- R-Value Work: 0.183 
- R-Value Observed: 0.185 
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 | 619 | Geobacillus stearothermophilus | Mutation(s): 0  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*TP*TP*TP*TP)-3' | 13 | Geobacillus stearothermophilus | |||
Sequence AnnotationsExpand | |||||
|
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
5'-D(*CP*AP*AP*(FAX)*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3' | 15 | Geobacillus stearothermophilus | |||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SO4 Query on SO4 | E [auth A], F [auth A], G [auth A], H [auth A], I [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
MG Query on MG | J [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
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: 2.20 Å
- R-Value Free: 0.217 
- R-Value Work: 0.183 
- R-Value Observed: 0.185 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 88.452 | α = 90 |
b = 93.726 | β = 90 |
c = 105.265 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2013-04-17  Deposition Author(s): Gehrke, T.H., Lischke, U., Arnold, S., Schneider, S., Carell, T.
Revision History (Full details and data files)
- Version 1.0: 2013-04-17
Type: Initial release - Version 1.1: 2013-05-22
Changes: Database references, Structure summary - Version 1.2: 2013-05-29
Changes: Database references - Version 1.3: 2013-07-03
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: 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