1RZT Transferase Dna date Dec 29, 2003
title Crystal Structure Of Dna Polymerase Lambda Complexed With A Nucleotide Gap Dna Molecule
authors L.C.Pedersen, M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.Blanco, T.A.
compound source
Molecule: 5'-D(Cpgpgpcpapapcpgpcpapc)-3'
Chain: B, F, J, N
Engineered: Yes
Other_details: Template Dna
Synthetic: Yes

Molecule: 5'-D(Gptpgpcpg)-3'
Chain: C, G, K, O
Engineered: Yes
Other_details: Upstream Primer Dna

Synthetic: Yes

Molecule: 5'-D(Pgpcpcpg)-3'
Chain: D, H, L, P
Engineered: Yes
Other_details: Downstream Primer Dna

Synthetic: Yes

Molecule: Dna Polymerase Lambda
Chain: A, E, I, M
Fragment: Catalytic Domain Of Polymerase Lambda
Synonym: Pol Lambda, Dna Polymerase Kappa, Dna Polymerase B Beta2;
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Poll
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-22b
symmetry Space Group: P 21 21 2
R_factor 0.227 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
191.321 99.034 104.838 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand EDO, NA enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 1XSN, 1XSP
Gene
Ontology
ChainFunctionProcessComponent
A, M, I, E


Primary referenceA structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology., Garcia-Diaz M, Bebenek K, Krahn JM, Blanco L, Kunkel TA, Pedersen LC, Mol Cell 2004 Feb 27;13(4):561-72. PMID:14992725
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (264 Kb) [Save to disk]
  • Biological Unit Coordinates (1rzt.pdb1.gz) 69 Kb
  • Biological Unit Coordinates (1rzt.pdb2.gz) 65 Kb
  • Biological Unit Coordinates (1rzt.pdb3.gz) 66 Kb
  • Biological Unit Coordinates (1rzt.pdb4.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 1RZT
  • CSU: Contacts of Structural Units for 1RZT
  • Likely Quarternary Molecular Structure file(s) for 1RZT
  • Structure Factors (1672 Kb)
  • Retrieve 1RZT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RZT from S2C, [Save to disk]
  • Re-refined 1rzt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RZT in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1RZT
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1RZT, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rzta1, region A:249-328 [Jmol] [rasmolscript] [script source]
        - Domain d1rzta2, region A:329-385 [Jmol] [rasmolscript] [script source]
        - Domain d1rzta3, region A:386-575 [Jmol] [rasmolscript] [script source]
        - Domain d1rzte1, region E:250-328 [Jmol] [rasmolscript] [script source]
        - Domain d1rzte2, region E:329-385 [Jmol] [rasmolscript] [script source]
        - Domain d1rzte3, region E:386-575 [Jmol] [rasmolscript] [script source]
        - Domain d1rzti1, region I:250-328 [Jmol] [rasmolscript] [script source]
        - Domain d1rzti2, region I:329-385 [Jmol] [rasmolscript] [script source]
        - Domain d1rzti3, region I:386-575 [Jmol] [rasmolscript] [script source]
        - Domain d1rztm1, region M:249-328 [Jmol] [rasmolscript] [script source]
        - Domain d1rztm2, region M:329-385 [Jmol] [rasmolscript] [script source]
        - Domain d1rztm3, region M:386-575 [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1rzt_P] [1rzt_H] [1rzt_N] [1rzt] [1rzt_G] [1rzt_O] [1rzt_C] [1rzt_J] [1rzt_A] [1rzt_D] [1rzt_F] [1rzt_E] [1rzt_B] [1rzt_L] [1rzt_K] [1rzt_M] [1rzt_I]
  • SWISS-PROT database: [Q9UGP5]
  • Domain organization of [DPOLL_HUMAN] by SWISSPFAM
  • Domains found in 1RZT: [HhH1] [POLXc ] by SMART
  • Other resources with information on 1RZT
  • Community annotation for 1RZT at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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