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- PDB-1dpi: STRUCTURE OF LARGE FRAGMENT OF ESCHERICHIA COLI DNA POLYMERASE I ... -

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Basic information

Entry
Database: PDB / ID: 1dpi
TitleSTRUCTURE OF LARGE FRAGMENT OF ESCHERICHIA COLI DNA POLYMERASE I COMPLEXED WITH D/TMP
ComponentsDNA POLYMERASE I KLENOW FRAGMENT
KeywordsNUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


5'-3' exonuclease activity / double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / base-excision repair / DNA-templated DNA replication / double-strand break repair / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair ...5'-3' exonuclease activity / double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / base-excision repair / DNA-templated DNA replication / double-strand break repair / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA binding / cytosol / cytoplasm
Similarity search - Function
3'-5' exonuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / DNA polymerase 1 / 3'-5' exonuclease / 3'-5' exonuclease domain ...3'-5' exonuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / DNA polymerase 1 / 3'-5' exonuclease / 3'-5' exonuclease domain / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / PIN-like domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsBeese, L. / Ollis, D. / Steitz, T.
Citation
Journal: Nature / Year: 1985
Title: Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP.
Authors: Ollis, D.L. / Brick, P. / Hamlin, R. / Xuong, N.G. / Steitz, T.A.
#1: Journal: Nature / Year: 1985
Title: Domain of E. Coli DNA Polymerase I Showing Sequence Homology to T7 DNA Polymerase
Authors: Ollis, D.L. / Kline, C. / Steitz, T.A.
#2: Journal: J.Mol.Biol. / Year: 1983
Title: Crystallization and 7 Angstroms Resolution Electron Density Map of the Large Fragment of Escherichia Coli DNA Polymerase I
Authors: Brick, P. / Ollis, D. / Steitz, T.A.
#3: Journal: J.Biol.Chem. / Year: 1982
Title: Nucleotide Sequence of the Escherichia Coli Pola Gene and Primary Structure of DNA Polymerase I
Authors: Joyce, C.M. / Kelley, W.S. / Grindley, N.D.F.
#4: Journal: J.Biol.Chem. / Year: 1982
Title: Escherichia Coli DNA Polymerase I. Sequence Characterization and Secondary Structure Prediction
Authors: Brown, W.E. / Stump, K.H. / Kelley, W.S.
History
DepositionAug 11, 1987Processing site: BNL
Revision 1.0Oct 16, 1987Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA POLYMERASE I KLENOW FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2272
Polymers68,1621
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.900, 102.900, 85.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein DNA POLYMERASE I KLENOW FRAGMENT / Coordinate model: Cα atoms only


Mass: 68161.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: T7 / Plasmid: T7 / Gene (production host): T7 / References: UniProt: P00582, DNA-directed DNA polymerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.07 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6 / Method: vapor diffusion / Details: Brick, P., (1983) J.Mol.Biol., 166, 453.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %protein1drop
21.1-1.2 Msodium citrate1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 20000 / Num. measured all: 80000 / Rmerge(I) obs: 0.05-0.006

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.2 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms546 0 1 0 547
Refinement
*PLUS
Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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