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- PDB-5j2e: Ternary complex crystal structure of DNA polymerase Beta with C:T... -

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Basic information

Entry
Database: PDB / ID: 5j2e
TitleTernary complex crystal structure of DNA polymerase Beta with C:T mismatch at the primer terminus
Components
  • DNA polymerase beta
  • Downstream Primer Strand
  • Primer Strand
  • Template StrandTranscription (biology)
KeywordsTransferase/DNA / DNA Polymerase Beta / mismatch extension / Ternary complex / Transferase-DNA complex
Function / homology
Function and homology information


immunoglobulin heavy chain V-D-J recombination / base-excision repair, DNA ligation / base-excision repair, base-free sugar-phosphate removal / Lyases, Carbon-oxygen lyases, Other carbon-oxygen lyases / base-excision repair, gap-filling / homeostasis of number of cells / pyrimidine dimer repair / lymph node development / salivary gland morphogenesis / somatic hypermutation of immunoglobulin genes ...immunoglobulin heavy chain V-D-J recombination / base-excision repair, DNA ligation / base-excision repair, base-free sugar-phosphate removal / Lyases, Carbon-oxygen lyases, Other carbon-oxygen lyases / base-excision repair, gap-filling / homeostasis of number of cells / pyrimidine dimer repair / lymph node development / salivary gland morphogenesis / somatic hypermutation of immunoglobulin genes / spleen development / response to hyperoxia / DNA-(apurinic or apyrimidinic site) endonuclease activity / response to gamma radiation / spindle microtubule / DNA-dependent DNA replication / base-excision repair / intrinsic apoptotic signaling pathway in response to DNA damage / lyase activity / neuron apoptotic process / double-strand break repair via nonhomologous end joining / microtubule / microtubule binding / in utero embryonic development / response to ethanol / damaged DNA binding / aging / DNA-directed DNA polymerase / protein deubiquitination / DNA-directed DNA polymerase activity / inflammatory response / DNA repair / cellular response to DNA damage stimulus / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm
DNA polymerase family X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix DNA-binding motif, class 1 / DNA-directed DNA polymerase X / DNA polymerase family X, binding site / DNA polymerase lambda lyase domain superfamily / DNA polymerase beta, palm domain / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / Fingers domain of DNA polymerase lambda ...DNA polymerase family X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix DNA-binding motif, class 1 / DNA-directed DNA polymerase X / DNA polymerase family X, binding site / DNA polymerase lambda lyase domain superfamily / DNA polymerase beta, palm domain / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / Fingers domain of DNA polymerase lambda / Helix-hairpin-helix domain / DNA polymerase beta thumb / DNA polymerase beta palm / DNA polymerase family X, beta-like / DNA polymerase lambda, fingers domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
DNA polymerase beta
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBatra, V.K. / Wilson, S.H.
CitationJournal: Structure / Year: 2016
Title: Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism.
Authors: Batra, V.K. / Beard, W.A. / Pedersen, L.C. / Wilson, S.H.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase beta
T: Template Strand
P: Primer Strand
D: Downstream Primer Strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,40614
Polymers47,6674
Non-polymers73910
Water6,467359
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-134 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)50.940, 79.940, 55.500
Angle α, β, γ (deg.)90.000, 107.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide DNA polymerase beta /


Mass: 38241.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Plasmid: pWL-11 / Production host: Escherichia coli (E. coli) / Strain (production host): Tap56
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases, Carbon-oxygen lyases, Other carbon-oxygen lyases

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DNA chain , 3 types, 3 molecules TPD

#2: DNA chain Template Strand / Transcription (biology)


Mass: 4813.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Primer Strand


Mass: 3076.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain Downstream Primer Strand


Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 369 molecules

#5: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Nov 15, 2005 / Details: Viramax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 24361 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 8.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.7 / % possible all: 97.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNS1.1refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FMS
Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.292 2051 8.3 %
Rwork0.2392 --
Obs-20416 82.3 %
Solvent computationBsol: 43.9663 Å2
Displacement parametersBiso max: 61.6 Å2 / Biso mean: 26.4381 Å2 / Biso min: 7.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.946 Å20 Å2-1.549 Å2
2---1.213 Å20 Å2
3---3.159 Å2
Refinement stepCycle: final / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 629 37 359 3637
Biso mean--19.71 29.51 -
Num. residues----357
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
c_mcbond_it1.3361.5
c_scbond_it1.9292
c_mcangle_it2.042
c_scangle_it2.7582.5
LS refinement shellResolution: 2.1→2.23 Å
RfactorNum. reflection% reflection
Rfree0.351 377 9.8 %
Rwork0.292 3465 -
Obs--93.7 %
Xplor fileSerial no: 1 / Param file: CTU.param

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