3TAP
Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-3) Position
- PDB DOI: https://doi.org/10.2210/pdb3TAP/pdb
- NAKB: 3TAP
- Classification: TRANSFERASE/DNA
- Organism(s): Geobacillus
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No 
- Deposited: 2011-08-04 Released: 2011-10-19 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.66 Å
- R-Value Free: 0.202 
- R-Value Work: 0.176 
- R-Value Observed: 0.177 
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 | 592 | Geobacillus | Mutation(s): 0  EC: 2.7.7.7 | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
5'-D(*G*CP*GP*AP*TP*CP*AP*CP*GP*CP*AP*C)-3' | 12 | N/A | |||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SO4 Query on SO4 | G [auth A], H [auth A], I [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
MG Query on MG | F [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: 1.66 Å
- R-Value Free: 0.202 
- R-Value Work: 0.176 
- R-Value Observed: 0.177 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 87.66 | α = 90 |
b = 93.27 | β = 90 |
c = 105.7 | γ = 90 |
Software Name | Purpose |
---|---|
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
REFMAC | phasing |
Entry History 
Deposition Data
- Released Date: 2011-10-19  Deposition Author(s): Wang, W., Beese, L.S.
Revision History (Full details and data files)
- Version 1.0: 2011-10-19
Type: Initial release - Version 1.1: 2011-11-16
Changes: Database references - Version 1.2: 2014-04-02
Changes: Source and taxonomy - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary