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- PDB-3e0j: X-ray structure of the complex of regulatory subunits of human DN... -

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Basic information

Entry
Database: PDB / ID: 3e0j
TitleX-ray structure of the complex of regulatory subunits of human DNA polymerase delta
Components
  • DNA polymerase subunit delta-2
  • DNA polymerase subunit delta-3
KeywordsTRANSFERASE / DNA Polymerase Delta / p66 subunit / p50 subunit / human / DNA replication / DNA-directed DNA polymerase / Nucleotidyltransferase / Nucleus / Polymorphism / Phosphoprotein
Function / homology
Function and homology information


delta DNA polymerase complex / DNA synthesis involved in UV-damage excision repair / zeta DNA polymerase complex / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / nucleotide-excision repair, DNA gap filling / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) ...delta DNA polymerase complex / DNA synthesis involved in UV-damage excision repair / zeta DNA polymerase complex / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / nucleotide-excision repair, DNA gap filling / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / DNA strand elongation involved in DNA replication / DNA synthesis involved in DNA repair / DNA biosynthetic process / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / error-prone translesion synthesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein-macromolecule adaptor activity / DNA replication / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #430 / Purple Acid Phosphatase; chain A, domain 2 - #50 / DNA polymerase delta, p66 (Cdc27) subunit, wHTH domain / DNA polymerase delta subunit 3 / DNA polymerase delta subunit 3 superfamily / DNA polymerase subunit Cdc27 / DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / DNA polymerase delta/II small subunit family ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #430 / Purple Acid Phosphatase; chain A, domain 2 - #50 / DNA polymerase delta, p66 (Cdc27) subunit, wHTH domain / DNA polymerase delta subunit 3 / DNA polymerase delta subunit 3 superfamily / DNA polymerase subunit Cdc27 / DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / DNA polymerase delta/II small subunit family / 50s Ribosomal Protein L17; Chain: A, / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / Purple Acid Phosphatase; chain A, domain 2 / 4-Layer Sandwich / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA polymerase delta subunit 2 / DNA polymerase delta subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 3 Å
AuthorsBaranovskiy, A.G. / Babayeva, N.D. / Pavlov, Y.I. / Vassylyev, D.G. / Tahirov, T.H.
Citation
Journal: Cell Cycle / Year: 2008
Title: X-ray structure of the complex of regulatory subunits of human DNA polymerase delta.
Authors: Baranovskiy, A.G. / Babayeva, N.D. / Liston, V.G. / Rogozin, I.B. / Koonin, E.V. / Pavlov, Y.I. / Vassylyev, D.G. / Tahirov, T.H.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization and preliminary crystallographic analysis of the complex of the second and third regulatory subunits of human Pol delta.
Authors: Baranovskiy, A.G. / Babayeva, N.D. / Pavlov, Y.I. / Tahirov, T.H.
History
DepositionJul 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 21, 2020Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all ..._reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase subunit delta-2
B: DNA polymerase subunit delta-3
C: DNA polymerase subunit delta-2
D: DNA polymerase subunit delta-3
E: DNA polymerase subunit delta-2
F: DNA polymerase subunit delta-3
G: DNA polymerase subunit delta-2
H: DNA polymerase subunit delta-3


Theoretical massNumber of molelcules
Total (without water)273,8318
Polymers273,8318
Non-polymers00
Water1,09961
1
G: DNA polymerase subunit delta-2
H: DNA polymerase subunit delta-3


Theoretical massNumber of molelcules
Total (without water)68,4582
Polymers68,4582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-30 kcal/mol
Surface area22510 Å2
MethodPISA
2
E: DNA polymerase subunit delta-2
F: DNA polymerase subunit delta-3


Theoretical massNumber of molelcules
Total (without water)68,4582
Polymers68,4582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-30 kcal/mol
Surface area22530 Å2
MethodPISA
3
C: DNA polymerase subunit delta-2
D: DNA polymerase subunit delta-3


Theoretical massNumber of molelcules
Total (without water)68,4582
Polymers68,4582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-29 kcal/mol
Surface area22560 Å2
MethodPISA
4
A: DNA polymerase subunit delta-2
B: DNA polymerase subunit delta-3


Theoretical massNumber of molelcules
Total (without water)68,4582
Polymers68,4582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-27 kcal/mol
Surface area23260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.128, 248.535, 103.461
Angle α, β, γ (deg.)90.00, 106.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA polymerase subunit delta-2 / / DNA polymerase subunit delta p50


Mass: 52224.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P49005, DNA-directed DNA polymerase
#2: Protein
DNA polymerase subunit delta-3 / / DNA polymerase subunit delta p66


Mass: 16233.576 Da / Num. of mol.: 4 / Fragment: residues 1-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: Q15054
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 4.27 Å3/Da / Density % sol: 71.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM imidazole, pH 6.5, 450 mM sodium acetate, 5 mM tris(2-carboxyethyl)phosphine hydrochloride (TCEP), and 1%(v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 31, 2007 / Details: Osmic VariMaxTM HR mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 85645 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 8304 / % possible all: 90.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 3→29.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3380250.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: fourfold ncs restrained
RfactorNum. reflection% reflectionSelection details
Rfree0.281 4224 5.1 %RANDOM
Rwork0.257 ---
obs0.257 83574 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.0811 Å2 / ksol: 0.316466 e/Å3
Displacement parametersBiso mean: 60.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å25.22 Å2
2---0.86 Å20 Å2
3----0.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.51 Å
Luzzati d res low-5 Å
Luzzati sigma a1.15 Å1.08 Å
Refinement stepCycle: LAST / Resolution: 3→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17092 0 0 61 17153
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.722
X-RAY DIFFRACTIONc_scbond_it1.532
X-RAY DIFFRACTIONc_scangle_it2.62.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.433 665 5.1 %
Rwork0.429 12492 -
obs-12492 86.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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