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- PDB-3cq8: Ternary complex of the L415F mutant RB69 exo(-)polymerase -

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Basic information

Entry
Database: PDB / ID: 3cq8
TitleTernary complex of the L415F mutant RB69 exo(-)polymerase
Components
  • DNA (5'-D(*DAP*DCP*DAP*DGP*DGP*DTP*DAP*DAP*DGP*DCP*DAP*DGP*DTP*DCP*DCP*DGP*DCP*DG)-3')
  • DNA (5'-D(*DGP*DCP*DGP*DGP*DAP*DCP*DTP*DGP*DCP*DTP*DTP*DAP*DCP*DC)-3')
  • DNA polymerase
KeywordsTransferase/DNA / B family polymerase fold / DNA replication / DNA-binding / DNA-directed DNA polymerase / Exonuclease / Hydrolase / Nuclease / Nucleotidyltransferase / Transferase / Transferase-DNA COMPLEX
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase ...DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhong, X. / Pedersen, L.C. / Kunkel, T.A.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity.
Authors: Zhong, X. / Pedersen, L.C. / Kunkel, T.A.
History
DepositionApr 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
T: DNA (5'-D(*DAP*DCP*DAP*DGP*DGP*DTP*DAP*DAP*DGP*DCP*DAP*DGP*DTP*DCP*DCP*DGP*DCP*DG)-3')
P: DNA (5'-D(*DGP*DCP*DGP*DGP*DAP*DCP*DTP*DGP*DCP*DTP*DTP*DAP*DCP*DC)-3')
A: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,56416
Polymers114,4973
Non-polymers1,06813
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-112 kcal/mol
Surface area43250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.840, 117.006, 127.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules TP

#1: DNA chain DNA (5'-D(*DAP*DCP*DAP*DGP*DGP*DTP*DAP*DAP*DGP*DCP*DAP*DGP*DTP*DCP*DCP*DGP*DCP*DG)-3')


Mass: 5550.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template strand
#2: DNA chain DNA (5'-D(*DGP*DCP*DGP*DGP*DAP*DCP*DTP*DGP*DCP*DTP*DTP*DAP*DCP*DC)-3')


Mass: 4256.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: dideoxy terminated primer strand

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Protein , 1 types, 1 molecules A

#3: Protein DNA polymerase / Gp43


Mass: 104689.156 Da / Num. of mol.: 1 / Fragment: RB69 polymerase / Mutation: L415F, D222A, D327A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage (virus) / Strain: RB69 / Gene: 43 / Plasmid: PCW50 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q38087, DNA-directed DNA polymerase

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Non-polymers , 5 types, 446 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 220mM CaCl2, 25% monometheyl ether PEG350, and 50mM Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Components of the solutions
IDNameCrystal-IDSol-ID
1CaCl211
2monometheyl ether PEG35011
3Tris-HCL11
4CaCl212
5monometheyl ether PEG35012
6Tris-HCL12

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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: Oct 12, 2006
RadiationMonochromator: VariMax HF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 42387 / Num. obs: 42387 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.076 / Net I/σ(I): 17.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 4200 / Rsym value: 0.51 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IG9

1ig9


Resolution: 2.5→25.7 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 563362.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1702 5 %RANDOM
Rwork0.212 ---
all0.212 34008 --
obs0.212 34008 79.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.5535 Å2 / ksol: 0.300453 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→25.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7345 650 56 433 8484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.442 243 5.5 %
Rwork0.326 4153 -
obs--62.7 %
Xplor fileSerial no: 1 / Param file: all.par / Topol file: all.top

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