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- PDB-4f5n: Open ternary complex of R283K DNA polymerase beta with a metal fr... -

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Basic information

Entry
Database: PDB / ID: 4f5n
TitleOpen ternary complex of R283K DNA polymerase beta with a metal free dCTP analog
Components
  • DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*GP*G)-3')
  • DNA polymerase beta
KeywordsTransferase / Lyase/DNA / Lyase-DNA complex
Function / homology
Function and homology information


Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / POLB-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / POLB-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / response to hyperoxia / lymph node development / salivary gland morphogenesis / somatic hypermutation of immunoglobulin genes / spleen development / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / 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 / DNA-templated DNA replication / intrinsic apoptotic signaling pathway in response to DNA damage / neuron apoptotic process / response to ethanol / microtubule binding / in utero embryonic development / DNA-directed DNA polymerase / damaged DNA binding / microtubule / DNA-directed DNA polymerase activity / Ub-specific processing proteases / lyase activity / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-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 ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-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 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase, domain 2 / 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
Chem-6CF / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFreudenthal, B.D. / Beard, W.A. / Wilson, S.H.
CitationJournal: Structure / Year: 2012
Title: Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly.
Authors: Freudenthal, B.D. / Beard, W.A. / Wilson, S.H.
History
DepositionMay 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase beta
T: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
P: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
D: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2508
Polymers47,6804
Non-polymers5704
Water10,142563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-60 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.322, 79.181, 54.857
Angle α, β, γ (deg.)90.00, 105.53, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHe biological assembly is a monomer in each asymmetric unit.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase beta


Mass: 38213.656 Da / Num. of mol.: 1 / Mutation: R283K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Plasmid: pWL11 / 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 DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 4869.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide from IDT / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')


Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide from IDT / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*CP*GP*G)-3')


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

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Non-polymers , 3 types, 567 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-6CF / 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine


Mass: 501.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16F2N3O12P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50mM Imidazole, 350mM Sodium Acetate, 18% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Sep 26, 2011 / Details: Mirrors
RadiationMonochromator: mirrors VarimaxHF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→28 Å / Num. all: 209537 / Num. obs: 209537 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.047
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.861.70.2293190.8
1.86-1.942.70.1885198.3
1.94-2.033.30.1447.9199.9
2.03-2.1340.125101100
2.13-2.274.80.113141100
2.27-2.445.50.09518.31100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7_650)refinement
CNSrefinement
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ISB.pdb

3isb


Resolution: 1.8→22.098 Å / SU ML: 0.26 / Isotropic thermal model: Restrained / σ(F): 0 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 4016 10.1 %Random
Rwork0.1871 ---
all0.202 39766 --
obs0.1903 39766 95.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.78 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1-2.641 Å2-0 Å22.2336 Å2
2--0.738 Å20 Å2
3----3.379 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2577 632 33 563 3805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083371
X-RAY DIFFRACTIONf_angle_d1.0274674
X-RAY DIFFRACTIONf_dihedral_angle_d19.1311312
X-RAY DIFFRACTIONf_chiral_restr0.057513
X-RAY DIFFRACTIONf_plane_restr0.003486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7981-1.81930.32631070.2572974X-RAY DIFFRACTION74
1.8193-1.84150.32671170.24541028X-RAY DIFFRACTION79
1.8415-1.86480.2951200.23231067X-RAY DIFFRACTION85
1.8648-1.88930.2891350.22771154X-RAY DIFFRACTION88
1.8893-1.91520.21781220.2211115X-RAY DIFFRACTION91
1.9152-1.94250.2931420.21751212X-RAY DIFFRACTION92
1.9425-1.97150.3051400.22081185X-RAY DIFFRACTION94
1.9715-2.00230.27791400.20071238X-RAY DIFFRACTION95
2.0023-2.03510.23741420.19351232X-RAY DIFFRACTION97
2.0351-2.07010.24941310.19231266X-RAY DIFFRACTION98
2.0701-2.10780.23391430.1951256X-RAY DIFFRACTION99
2.1078-2.14830.27831420.20391254X-RAY DIFFRACTION98
2.1483-2.19210.25531400.20211282X-RAY DIFFRACTION98
2.1921-2.23970.25241380.19571259X-RAY DIFFRACTION98
2.2397-2.29170.23611510.19061267X-RAY DIFFRACTION99
2.2917-2.3490.23691540.19631261X-RAY DIFFRACTION98
2.349-2.41240.23481240.19981266X-RAY DIFFRACTION98
2.4124-2.48330.2731230.20061289X-RAY DIFFRACTION98
2.4833-2.56340.24791450.2091252X-RAY DIFFRACTION98
2.5634-2.65480.22991460.20161269X-RAY DIFFRACTION98
2.6548-2.76090.24931450.20051262X-RAY DIFFRACTION99
2.7609-2.88630.231460.19151277X-RAY DIFFRACTION98
2.8863-3.03810.22481630.20211265X-RAY DIFFRACTION99
3.0381-3.2280.21941550.19171272X-RAY DIFFRACTION100
3.228-3.47630.18251440.17461303X-RAY DIFFRACTION100
3.4763-3.82450.18711330.16591305X-RAY DIFFRACTION100
3.8245-4.37420.17741390.1521302X-RAY DIFFRACTION100
4.3742-5.4970.16761520.16191300X-RAY DIFFRACTION100
5.497-22.10.19681370.18391338X-RAY DIFFRACTION100

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