3HWT | pdb_00003hwt

Ternary complex of DNA polymerase lambda bound to a two nucleotide gapped DNA substrate with a scrunched dA

• PDB DOI: https://doi.org/10.2210/pdb3HWT/pdb
• NAKB: 3HWT

• Classification: TRANSFERASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-06-18 Released: 2009-08-25 
• Deposition Author(s): Garcia-Diaz, M., Bebenek, K., Larrea, A.A., Pedersen, L.C., Kunkel, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.261 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.232 (DCC) 

Starting Model: experimental

Literature

Scrunching during DNA repair synthesis

Garcia-Diaz, M., Bebenek, K., Larrea, A.A., Havener, J.M., Perera, L., Krahn, J.M., Pedersen, L.C., Ramsden, D.A., Kunkel, T.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.68 kDa 
• Atom Count: 3,241 
• Modeled Residue Count: 341 
• Deposited Residue Count: 357 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase lambda	A	335	Homo sapiens	Mutation(s): 1  Gene Names: POLL EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGP5 (Homo sapiens) Explore Q9UGP5  Go to UniProtKB:  Q9UGP5
PHAROS:  Q9UGP5 GTEx:  ENSG00000166169

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3'	B [auth T]	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*GP*TP*AP*(2DT))-3'	C [auth P]	6	N/A

Entity ID: 4
Molecule	Chains	Length	Organism	Image
5'-D(P*GP*CP*CP*G)-3'	D	4	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D3T	E [auth A]	2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O13 P3 URGJWIFLBWJRMF-JGVFFNPUSA-N
EDO	H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.261 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.232 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.023	α = 90
b = 68.328	β = 90
c = 137.85	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Garcia-Diaz, M., Bebenek, K., Larrea, A.A., Pedersen, L.C., Kunkel, T.A.

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-09-25
  Changes: Derived calculations
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.5: 2023-09-06
  Changes: Data collection, Refinement description