1L3V
Crystal Structure of Bacillus DNA Polymerase I Fragment product complex with 15 base pairs of duplex DNA following addition of dTTP, dATP, dCTP, and dGTP residues.
- PDB DOI: https://doi.org/10.2210/pdb1L3V/pdb
- NAKB: 1L3V
- Classification: TRANSFERASE/DNA
- Organism(s): Geobacillus stearothermophilus
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2002-03-01 Released: 2003-03-25 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.71 Å
- R-Value Free: 0.234 
- R-Value Work: 0.206 
- R-Value Observed: 0.207 
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: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
DNA Polymerase I | C [auth A] | 580 | Geobacillus stearothermophilus | Mutation(s): 0  EC: 2.7.7.7 | |
UniProt | |||||
Find proteins for P52026 (Geobacillus stearothermophilus) Explore P52026  Go to UniProtKB:  P52026 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P52026 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*AP*CP*GP*TP*C)-3' | A [auth B] | 15 | N/A | ||
Sequence AnnotationsExpand | |||||
|
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
5'-D(*GP*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3' | B [auth C] | 16 | N/A | ||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SO4 Query on SO4 | F [auth A], G [auth A], H [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
MG Query on MG | I [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, E | sucrose | Oligosaccharide / Nutrient |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.71 Å
- R-Value Free: 0.234 
- R-Value Work: 0.206 
- R-Value Observed: 0.207 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 88.072 | α = 90 |
b = 93.378 | β = 90 |
c = 104.919 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | refinement |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2003-03-25  Deposition Author(s): Johnson, S.J., Taylor, J.S., Beese, L.S.
Revision History (Full details and data files)
- Version 1.0: 2003-03-25
Type: Initial release - Version 1.1: 2008-04-28
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-08-16
Changes: Data collection, Database references, Refinement description, Structure summary