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- PDB-1qsl: KLENOW FRAGMENT COMPLEXED WITH SINGLE-STRANDED SUBSTRATE AND EURO... -

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Basic information

Entry
Database: PDB / ID: 1qsl
TitleKLENOW FRAGMENT COMPLEXED WITH SINGLE-STRANDED SUBSTRATE AND EUROPIUM (III) ION
Components
  • 5'-D(*GP*CP*TP*TP*AP*CP*GP*C)-3'
  • DNA POLYMERASE I
KeywordsTRANSFERASE/DNA / EXONUCLEASE / TWO METAL IONS / SINGLE-STRANDED DNA / 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
EUROPIUM ION / DNA / DNA polymerase I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsBrautigam, C.A. / Aschheim, K. / Steitz, T.A.
Citation
Journal: Chem.Biol. / Year: 1999
Title: Structural elucidation of the binding and inhibitory properties of lanthanide (III) ions at the 3'-5' exonucleolytic active site of the Klenow fragment
Authors: Brautigam, C.A. / Aschheim, K. / Steitz, T.A.
#1: 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.
#2: 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
DepositionJun 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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Assembly

Deposited unit
B: 5'-D(*GP*CP*TP*TP*AP*CP*GP*C)-3'
A: DNA POLYMERASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7483
Polymers70,5962
Non-polymers1521
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.300, 103.300, 86.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Cell settingtetragonal
Space group name H-MP43

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Components

#1: DNA chain 5'-D(*GP*CP*TP*TP*AP*CP*GP*C)-3'


Mass: 2402.592 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CHEMICALLY SYNTHESIZED BY STANDARD PHOSPHORAMIDITE METHODOLOGY
#2: Protein DNA POLYMERASE I / E.C.2.7.7.7 / POL I


Mass: 68193.750 Da / Num. of mol.: 1 / Fragment: KLENOW FRAGMENT / 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): CJ376 / References: UniProt: P00582, DNA-directed DNA polymerase
#3: Chemical ChemComp-EU / EUROPIUM ION


Mass: 151.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Eu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 3.26 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.5 M SODIUM CITRATE AT 290 K, pH 5.60, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CITRATE11
2SODIUM CITRATE12
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %protein1drop
21.1-1.2 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9
DetectorType: ADSC / Detector: CCD / Date: May 17, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 45999 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.4
Reflection shellResolution: 2.2→2.23 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.346 / % possible all: 99.7
Reflection
*PLUS
Num. obs: 40431 / Num. measured all: 343566
Reflection shell
*PLUS
Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 2.2→20 Å / σ(F): 2 / Details: BULK-SOLVENT CORRECTION WAS APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 4134 10 %RANDOM
Rwork0.214 ---
obs0.214 40431 --
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4753 61 1 191 5006
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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