1XSP | pdb_00001xsp

Crystal Structure of human DNA polymerase lambda in complex with nicked DNA and pyrophosphate

• PDB DOI: https://doi.org/10.2210/pdb1XSP/pdb
• NAKB: 1XSP

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


• Deposited: 2004-10-19 Released: 2005-01-18 
• Deposition Author(s): Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Kunkel, T.A., Pedersen, L.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.242 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

A closed conformation for the Pol lambda catalytic cycle.

Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Kunkel, T.A., Pedersen, L.C.

(2005) Nat Struct Mol Biol 12: 97-98

• PubMed: 15608652 
• DOI: https://doi.org/10.1038/nsmb876
• Primary Citation Related Structures: 
  1XSL, 1XSN, 1XSP


• PubMed Abstract: 
  

  Pol lambda is a family X member believed to fill short gaps during DNA repair. Here we report crystal structures of Pol lambda representing three steps in filling a single-nucleotide gap. These structures indicate that, unlike other DNA polymerases, Pol lambda does not undergo large subdomain movements during catalysis, and they provide a clear characterization of the geometry and stereochemistry of the in-line nucleotidyl transfer reaction.

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Organizational Affiliation: 
• Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.38 kDa 
• Atom Count: 3,363 
• Modeled Residue Count: 349 
• Deposited Residue Count: 357 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase lambda	D [auth A]	335	Homo sapiens	Mutation(s): 1  Gene Names: POLL EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGP5 (Homo sapiens) Explore Q9UGP5  Go to UniProtKB:  Q9UGP5
PHAROS:  Q9UGP5 GTEx:  ENSG00000166169

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*GP*CP*CP*GP*TP*AP*CP*TP*G)-3'	A [auth T]	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*GP*TP*AP*CP*G)-3'	B [auth P]	7	N/A

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PPV	I [auth A]	PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N
NA	E [auth D], F [auth A], G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.242 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.845	α = 90
b = 62.758	β = 90
c = 140.72	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-18 
Deposition Author(s): Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Kunkel, T.A., Pedersen, L.C.

Revision History  

• Version 1.0: 2005-01-18
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2024-02-14
  Changes: Data collection