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- PDB-4f5r: Open and closed ternary complex of R283K DNA polymerase beta with... -

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Basic information

Entry
Database: PDB / ID: 4f5r
TitleOpen and closed ternary complex of R283K DNA polymerase beta with a dCTP analog in the same asymmetric unit
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 / homeostasis of number of cells / pyrimidine dimer repair / 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 / homeostasis of number of cells / pyrimidine dimer repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / 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 / microtubule binding / neuron apoptotic process / in utero embryonic development / microtubule / response to ethanol / damaged DNA binding / DNA-directed DNA polymerase / 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: 2.2 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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
B: DNA polymerase beta
D: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
P: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
T: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
C: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
G: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
F: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,67418
Polymers95,3608
Non-polymers1,31410
Water7,458414
1
A: DNA polymerase beta
D: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
P: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
T: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3379
Polymers47,6804
Non-polymers6575
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-47 kcal/mol
Surface area21280 Å2
MethodPISA
2
B: DNA polymerase beta
C: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
G: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
F: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3379
Polymers47,6804
Non-polymers6575
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-53 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.028, 79.446, 102.090
Angle α, β, γ (deg.)90.00, 96.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase beta


Mass: 38213.656 Da / Num. of mol.: 2 / 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, 6 molecules DCPGTF

#2: DNA chain DNA (5'-D(P*GP*TP*CP*GP*G)-3')


Mass: 1536.035 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Details: polydeoxyribonucleotide from IDT / Source: (synth.) synthetic construct (others)
#4: 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.: 2 / Source method: obtained synthetically / Details: polydeoxyribonucleotide from IDT / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 424 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / 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.: 2 / Source method: obtained synthetically / Formula: C10H16F2N3O12P3
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50mM Imidazole, 350mM Sodium Acetate, 16.5% 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: Jun 21, 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: 2.2→50 Å / Num. all: 263254 / Num. obs: 263254 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.136
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.2-2.285.80.7032.731100
2.28-2.375.90.5813.371100
2.37-2.485.90.5453.461100
2.48-2.615.90.4544.071100
2.61-2.7760.3415.171100
2.77-2.9960.2595.671100

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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 and 2FMS

3isb

2fms


Resolution: 2.2→21.36 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2776 1393 3.65 %Random
Rwork0.2097 ---
all0.2122 74621 --
obs0.2122 74621 85.78 %-
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.645 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.8979 Å2-0 Å2-0.2014 Å2
2---0.3574 Å2-0 Å2
3---6.2553 Å2
Refinement stepCycle: LAST / Resolution: 2.2→21.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5152 1264 68 414 6898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116779
X-RAY DIFFRACTIONf_angle_d1.19456
X-RAY DIFFRACTIONf_dihedral_angle_d21.5122621
X-RAY DIFFRACTIONf_chiral_restr0.0621028
X-RAY DIFFRACTIONf_plane_restr0.004979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.35021450.26263615X-RAY DIFFRACTION83
2.24-2.2830.33121440.25723371X-RAY DIFFRACTION77
2.283-2.32960.33781420.24943562X-RAY DIFFRACTION81
2.3296-2.38010.31331500.23953677X-RAY DIFFRACTION82
2.3801-2.43540.27951280.25583385X-RAY DIFFRACTION77
2.4354-2.49620.36631240.25463452X-RAY DIFFRACTION78
2.4962-2.56360.40731220.27743353X-RAY DIFFRACTION77
2.5636-2.63890.34531330.26163425X-RAY DIFFRACTION78
2.6389-2.7240.34611310.25783486X-RAY DIFFRACTION79
2.724-2.82110.33111220.2513467X-RAY DIFFRACTION77
2.8211-2.93380.29681230.24223484X-RAY DIFFRACTION79
2.9338-3.06690.32611400.233624X-RAY DIFFRACTION83
3.0669-3.22810.31851500.22764189X-RAY DIFFRACTION94
3.2281-3.42960.31071610.21524302X-RAY DIFFRACTION98
3.4296-3.69310.28721670.21434422X-RAY DIFFRACTION99
3.6931-4.06250.2191580.17094200X-RAY DIFFRACTION96
4.0625-4.64510.21341580.14744222X-RAY DIFFRACTION95
4.6451-5.83250.2081590.17564255X-RAY DIFFRACTION97
5.8325-21.36110.23191670.19574406X-RAY DIFFRACTION99

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