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- PDB-1jn3: FIDELITY PROPERTIES AND STRUCTURE OF M282L MUTATOR MUTANT OF DNA ... -

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Basic information

Entry
Database: PDB / ID: 1jn3
TitleFIDELITY PROPERTIES AND STRUCTURE OF M282L MUTATOR MUTANT OF DNA POLYMERASE: SUBTLE STRUCTURAL CHANGES INFLUENCE THE MECHANISM OF NUCLEOTIDE DISCRIMINATION
ComponentsDNA POLYMERASE BETA
KeywordsTRANSFERASE / DNA POLYMERASE BETA (Fragment) / mutant / NUCLEOTIDE DISCRIMINATION
Function / homology
Function and homology information


Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases ...Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / base-excision repair, gap-filling / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / response to gamma radiation / spindle microtubule / base-excision repair / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / in utero embryonic development / neuron apoptotic process / response to ethanol / microtubule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / inflammatory response / DNA damage response / apoptotic process / enzyme binding / protein-containing complex / DNA binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Beta Polymerase, domain 2 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.35 Å
AuthorsConn, D.A. / Sweasy, J.B. / Jaeger, J.
CitationJournal: Biochemistry / Year: 2001
Title: A DNA polymerase beta mutator mutant with reduced nucleotide discrimination and increased protein stability
Authors: Shah, A.M. / Conn, D.A. / Li, S.-X. / Capaldi, A. / Jaeger, J. / Sweasy, J.B.
History
DepositionJul 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 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
A: DNA POLYMERASE BETA


Theoretical massNumber of molelcules
Total (without water)29,1281
Polymers29,1281
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.540, 63.620, 37.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-493-

HOH

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Components

#1: Protein DNA POLYMERASE BETA / E.C.2.7.7.7 / BETANUCLEOTIDYLTRANSFERASE / Beta Polymerase


Mass: 29127.941 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 85 - 335 / Mutation: M282L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P06766, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG 3350, 5mM ammonium sulfate, 150mM sodium acetate, 50mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113.5 mg/mlprotein1drop
210 mMammonium sulfate1drop
30.1 MMES1drop
413-20.0 %PEG33501reservoir
550-300 mMsodium acetate1reservoir
650 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 10, 2000 / Details: Yale Mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→22.48 Å / Num. all: 11677 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 2.35→2.53 Å / % possible all: 73.6
Reflection
*PLUS
Num. obs: 11677 / Num. measured all: 89772 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 65.3 % / Rmerge(I) obs: 0.244

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.35→22.48 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1747770.54 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.5 / σ(I): 0.75 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1093 9.7 %RANDOM
Rwork0.215 ---
all0.221 11677 --
obs0.215 -93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.9086 Å2 / ksol: 0.281913 e/Å3
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1--11.06 Å20 Å20 Å2
2---9.59 Å20 Å2
3---20.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.35→22.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1969 0 0 185 2154
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1.5
LS refinement shellResolution: 2.35→2.54 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 144 10.1 %
Rwork0.239 1283 -
obs-1283 73.6 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 11677 / σ(F): 1.5 / % reflection Rfree: 9.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.297 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.239

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