4F2S
DNA Polymerase I Large Fragment complex 4
- PDB DOI: https://doi.org/10.2210/pdb4F2S/pdb
- NAKB: 4F2S
- Classification: Transferase/DNA
- Organism(s): Geobacillus kaustophilus HTA426, synthetic construct
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes 
- Deposited: 2012-05-08 Released: 2013-07-24 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.65 Å
- R-Value Free: 0.199 
- R-Value Work: 0.174 
- R-Value Observed: 0.175 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
DNA polymerase | A, B [auth D] | 592 | Geobacillus kaustophilus HTA426 | Mutation(s): 2  Gene Names: polA, GK2730 EC: 2.7.7.7 | |
UniProt | |||||
Find proteins for Q5KWC1 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KWC1  Go to UniProtKB:  Q5KWC1 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q5KWC1 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3') | C [auth B], E | 9 | synthetic construct | ||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') | D [auth C], F | 13 | synthetic construct | ||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CTP Query on CTP | I [auth A], J [auth D] | CYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O14 P3 PCDQPRRSZKQHHS-XVFCMESISA-N | |||
SO4 Query on SO4 | L [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
MN Query on MN | K [auth D] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-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 | G, H | sucrose | Oligosaccharide / Nutrient |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.65 Å
- R-Value Free: 0.199 
- R-Value Work: 0.174 
- R-Value Observed: 0.175 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 93.18 | α = 90 |
b = 108.59 | β = 90 |
c = 150.99 | γ = 90 |
Software Name | Purpose |
---|---|
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Entry History 
Deposition Data
- Released Date: 2013-07-24  Deposition Author(s): Wang, W., Beese, L.S.
Revision History (Full details and data files)
- Version 1.0: 2013-07-24
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary