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- PDB-1ksp: DNA polymerase I Klenow fragment (E.C.2.7.7.7) mutant/DNA complex -

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Basic information

Entry
Database: PDB / ID: 1ksp
TitleDNA polymerase I Klenow fragment (E.C.2.7.7.7) mutant/DNA complex
Components
  • DNA (5'-D(P*TP*TP*PST)-3')
  • PROTEIN (DNA POLYMERASE I-KLENOW FRAGMENT (E.C.2.7.7.7))
KeywordsTRANSFERASE/DNA / COMPLEX (DNA-BINDING PROTEIN-DNA) / EXONUCLEASE / PHOSPHOROTHIOATE / 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 / 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
DNA / DNA polymerase I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID-BODY REFINEMENT / Resolution: 2.3 Å
AuthorsBrautigam, C.A. / Steitz, T.A.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates.
Authors: Brautigam, C.A. / 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.
History
DepositionAug 19, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Feb 25, 1998Provider: 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 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,2084
Polymers69,0772
Non-polymers1312
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.560, 101.560, 85.250
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(P*TP*TP*PST)-3')


Mass: 883.687 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (DNA POLYMERASE I-KLENOW FRAGMENT (E.C.2.7.7.7)) / LARGE FRAGMENT


Mass: 68193.750 Da / Num. of mol.: 1 / Mutation: V324M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PCJ155 / Production host: Escherichia coli (E. coli) / Strain (production host): CJ 376 / Keywords: MUTATION: V324M / References: UniProt: P00582, DNA-directed DNA polymerase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 64 %
Crystal growpH: 5.8 / Details: 1.4 M NA CITRATE PH 5.8
Crystal
*PLUS
Density % sol: 64 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Brick, P., (1983) J. Mol. Biol., 166, 453.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.1-1.2 Msodium citrate1reservoir
220 mMPIPES1drop
31 mMdithiothreitol1drop
40.02 %1dropNaN3
510 mg/mlprotain1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 200444 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Rsym value: 0.064 / Net I/σ(I): 12.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.407 / % possible all: 96.3
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. obs: 31495 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Num. measured all: 200444 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.34 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: RIGID-BODY REFINEMENT
Starting model: IN-HOUSE HIGH-RESOLUTION STRUCTURE

Resolution: 2.3→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2
Details: ONLY THE THREE 3'-TERMINAL BASES OF THE DNA COULD BE MODELED INTO ELECTRON DENSITY. ONLY THE LAST PHOSPHATE IS MODIFIED.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3212 10 %RANDOM
Rwork0.193 ---
obs-31495 96.3 %-
Displacement parametersBiso mean: 38.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4753 61 2 210 5026
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.33 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.33 65 10 %
Rwork0.298 711 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2CHAD_PARAM.DNACHAD_TOP.DNA
X-RAY DIFFRACTION3NEWPARAM.EXP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.3301 / Rfactor Rwork: 0.2977

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