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- PDB-6p5c: Bacillus Fragment DNA polymerase mutant I716M -

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Basic information

Entry
Database: PDB / ID: 6p5c
TitleBacillus Fragment DNA polymerase mutant I716M
Components
  • DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*GP*TP*GP*AP*TP*CP*G)-3')
  • DNA polymerase I
KeywordsREPLICATION/DNA / Polymerase / REPLICATION / TRANSFERASE / REPLICATION-DNA complex
Function / homology
Function and homology information


double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
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 / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. ...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 / 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 / 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 polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsWu, E.Y.
CitationJournal: DNA Repair (Amst.) / Year: 2020
Title: The importance of Ile716 toward the mutagenicity of 8-Oxo-2'-deoxyguanosine with Bacillus fragment DNA polymerase.
Authors: Hamm, M.L. / Garcia, A.A. / Gilbert, R. / Johri, M. / Ricart, M. / Sholes, S.L. / Murray-Nerger, L.A. / Wu, E.Y.
History
DepositionMay 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,1797
Polymers71,7953
Non-polymers3844
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-63 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.217, 93.521, 105.279
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 2700.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*GP*CP*GP*TP*GP*AP*TP*CP*G)-3')


Mass: 2771.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein DNA polymerase I


Mass: 66322.086 Da / Num. of mol.: 1 / Mutation: I716M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: DPO1, polA / Plasmid: pET21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: D9N168, DNA-directed DNA polymerase
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.02 Å3/Da / Density % sol: 59.33 % / Description: ~0.1x0.1x0.4 mm rod
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 50% saturated ammonium sulfate, 100 mM MES, 2% methylpentanediol, 10 mM magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→70 Å / Num. obs: 44306 / % possible obs: 98.5 % / Redundancy: 3.9 % / Net I/σ(I): 14.62
Reflection shellResolution: 2.2→2.29 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 6.36 / Num. unique obs: 4436 / Rsym value: 0.314 / % possible all: 92.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.31 Å28.32 Å
Translation6.31 Å28.32 Å

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Processing

Software
NameVersionClassification
PHASER2.8.2phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L3S

1l3s


Resolution: 2.2→28.34 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.86 / SU B: 5.91 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.219
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 2134 4.9 %RANDOM
Rwork0.2277 ---
obs0.2299 41136 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 130.52 Å2 / Biso mean: 29.56 Å2 / Biso min: 9.96 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.2→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 366 20 144 5188
Biso mean--76.48 22.32 -
Num. residues----599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135167
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174740
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.6017060
X-RAY DIFFRACTIONr_angle_other_deg1.3421.63710986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0215580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26922.201268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79815876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8541538
X-RAY DIFFRACTIONr_chiral_restr0.0760.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025499
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021078
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.674 133 -
Rwork0.663 2487 -
all-2620 -
obs--80.12 %

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