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- PDB-1kln: DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1kln
TitleDNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX
Components
  • DNA (5'-D(*GP*CP*CP*GP*CP*GP*AP*GP*GP*C)-3')
  • DNA (5'-D(*GP*CP*CP*TP*CP*GP*CP*GP*GP*CP*GP*GP*C)-3')
  • PROTEIN (DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7))
KeywordsTRANSFERASE/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSFERASE-DNA COMPLEX
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 / cytoplasm / cytosol
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
DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsBeese, L.S. / Derbyshire, V. / Steitz, T.A.
Citation
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.
#1: Journal: Embo J. / Year: 1991
Title: Structural Basis for the 3'-5' Exonuclease Activity of Escherichia Coli DNA Polymerase I: A Two Metal Ion Mechanism
Authors: Beese, L.S. / Steitz, T.A.
#2: 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.
#3: 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
DepositionMay 24, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Nov 30, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*GP*CP*CP*TP*CP*GP*CP*GP*GP*CP*GP*GP*C)-3')
C: DNA (5'-D(*GP*CP*CP*GP*CP*GP*AP*GP*GP*C)-3')
A: PROTEIN (DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2244
Polymers75,1583
Non-polymers651
Water00
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: DNA chain DNA (5'-D(*GP*CP*CP*TP*CP*GP*CP*GP*GP*CP*GP*GP*C)-3')


Mass: 3969.561 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*CP*CP*GP*CP*GP*AP*GP*GP*C)-3')


Mass: 3071.006 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7))


Mass: 68117.680 Da / Num. of mol.: 1 / Mutation: D355A / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Keywords: MUTANT D355A / References: UniProt: P00582
#4: 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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 6.8 / Details: pH 6.80, VAPOR DIFFUSION, temperature 290.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NH4 SULFATE11
3CITRATE BUFFER11
4MG SULFATE11
5ZN SULFATE11
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion / pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110-12 mg/mlprotein1drop
235-40 %(w/v)satammonium sulfate1reservoir
3200 mMcitrate1reservoirpH6.8
420 mM1reservoirMgSO4
51 mM1reservoirZnSO4

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Data collection

DetectorType: UCSD MARK II / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 3.2→10 Å / Rfactor Rwork: 0.23
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 470 1 0 5171
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 10 Å / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg2.7

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