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- PDB-4xiu: Binary complex structure of Klenow fragment of Taq DNA polymerase... -

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Basic information

Entry
Database: PDB / ID: 4xiu
TitleBinary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant with DNA containing TTT overhang
Components
  • DNA polymerase I, thermostable
  • Synthetic oligonucleotide primer strand
  • Synthetic oligonucleotide template strand
KeywordsTRANSFERASE/DNA / protein-DNA complex / TRANSFERASE-DNA complex
Function / homology
Function and homology information


nucleoside binding / 5'-3' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Taq polymerase, thermostable, exonuclease region / Taq polymerase, 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 / Taq DNA Polymerase; Chain T, domain 4 ...Taq polymerase, thermostable, exonuclease region / Taq polymerase, 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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 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 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsWu, E.Y.
CitationJournal: Biochemistry / Year: 2015
Title: A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase.
Authors: Wu, E.Y. / Walsh, A.R. / Materne, E.C. / Hiltner, E.P. / Zielinski, B. / Miller, B.R. / Mawby, L. / Modeste, E. / Parish, C.A. / Barnes, W.M. / Kermekchiev, M.B.
History
DepositionJan 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Synthetic oligonucleotide primer strand
C: Synthetic oligonucleotide template strand
A: DNA polymerase I, thermostable
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8364
Polymers68,8123
Non-polymers241
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-20 kcal/mol
Surface area25310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.030, 110.030, 90.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Detailsbiological unit is the same as asym.

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Components

#1: DNA chain Synthetic oligonucleotide primer strand


Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic oligonucleotide / Source: (synth.) synthetic construct (others)
#2: DNA chain Synthetic oligonucleotide template strand


Mass: 4328.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic oligonucleotide / Source: (synth.) synthetic construct (others)
#3: Protein DNA polymerase I, thermostable / Taq polymerase 1


Mass: 60865.887 Da / Num. of mol.: 1
Fragment: Klenow fragment of DNA polymerase I from Thermus aquatics
Mutation: I707L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: polA, pol1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19821, DNA-directed DNA polymerase
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 21497 / Num. obs: 21497 / % possible obs: 96.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.12 / Χ2: 2.684 / Net I/av σ(I): 21.394 / Net I/σ(I): 11.55 / Num. measured all: 102057
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.96 % / Num. unique all: 1322 / Χ2: 3.7 / Rejects: 0 / % possible all: 97.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.15 Å47.64 Å
Translation7.15 Å47.64 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KTQ

4ktq


Resolution: 2.5→47.64 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.2965 / WRfactor Rwork: 0.2231 / FOM work R set: 0.777 / SU B: 12.317 / SU ML: 0.27 / SU R Cruickshank DPI: 1.0086 / SU Rfree: 0.3542 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.009 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2861 1075 5 %RANDOM
Rwork0.223 20422 --
obs0.2261 20422 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 164.39 Å2 / Biso mean: 52.506 Å2 / Biso min: 22.05 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.5→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4191 530 1 1 4723
Biso mean--44.97 34 -
Num. residues----565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0184873
X-RAY DIFFRACTIONr_bond_other_d0.0010.024442
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.8796720
X-RAY DIFFRACTIONr_angle_other_deg0.876310188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41222.461191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.36515712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7241547
X-RAY DIFFRACTIONr_chiral_restr0.0720.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215152
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021115
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 77 -
Rwork0.324 1478 -
all-1555 -
obs--97.31 %

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