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- PDB-1kfd: CRYSTAL STRUCTURES OF THE KLENOW FRAGMENT OF DNA POLYMERASE I COM... -

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Entry
Database: PDB / ID: 1kfd
TitleCRYSTAL STRUCTURES OF THE KLENOW FRAGMENT OF DNA POLYMERASE I COMPLEXED WITH DEOXYNUCLEOSIDE TRIPHOSPHATE AND PYROPHOSPHATE
ComponentsDNA POLYMERASE I KLENOW FRAGMENT
KeywordsNUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


5'-3' exonuclease activity / 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 ...5'-3' exonuclease activity / 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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 ...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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 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 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / DNA polymerase I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3.9 Å
AuthorsBeese, L.S. / Friedman, J.M. / Steitz, T.A.
Citation
Journal: Biochemistry / Year: 1993
Title: Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate.
Authors: Beese, L.S. / Friedman, J.M. / Steitz, T.A.
#1: Journal: Science / Year: 1993
Title: Structure of DNA Polymerase I Klenow Fragment Bound to Duplex DNA
Authors: Beese, L.S. / Derbyshire, V. / Steitz, T.A.
#2: Journal: Embo J. / Year: 1991
Title: Structural Basis for the 3'-5' Exonuclease Activity of E. Coli DNA Polymerase F: A Two Metal Ion Mechanism
Authors: Beese, L.S. / Steitz, T.A.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Co-Crystal Structure of an Editing Complex of Klenow Fragment with DNA
Authors: Freemont, P.S. / Friedman, J.M. / Beese, L.S. / Steitz, T.A.
#4: 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.
History
DepositionSep 23, 1993Processing site: BNL
Revision 1.0Jun 22, 1994Provider: 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)68,6452
Polymers68,1621
Non-polymers4831
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.300, 104.300, 86.000
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


Mass: 68161.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P00582, DNA-directed DNA polymerase
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.14 %
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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 3.9 Å
Refinement stepCycle: LAST / Highest resolution: 3.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4451 0 28 0 4479

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