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- PDB-4dtu: RB69 DNA Polymerase Ternary Complex with dGTP Opposite an Abasic ... -

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Basic information

Entry
Database: PDB / ID: 4dtu
TitleRB69 DNA Polymerase Ternary Complex with dGTP Opposite an Abasic Site and ddC/dG as the Penultimate Base-pair
Components
  • DNA polymerase
  • DNA primer
  • DNA tempalte
KeywordsTransferase/DNA / abasic site / THF / RB69pol / dGTP / Transferase-DNA complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 3'-5' exonuclease activity / DNA-templated DNA replication / 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 / : ...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-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Helix Hairpins / 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
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsXia, S. / Wang, J. / Konigsberg, W.H.
CitationJournal: Biochemistry / Year: 2012
Title: Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA.
Authors: Xia, S. / Vashishtha, A. / Bulkley, D. / Eom, S.H. / Wang, J. / Konigsberg, W.H.
History
DepositionFeb 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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
T: DNA tempalte
P: DNA primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,59910
Polymers113,8513
Non-polymers7487
Water14,340796
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-79 kcal/mol
Surface area42700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.925, 120.012, 130.569
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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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase / Gp43


Mass: 104490.945 Da / Num. of mol.: 1 / Mutation: D222A, D327A, L561A, S565G, Y567A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38087, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA tempalte


Mass: 5408.480 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA primer


Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 803 molecules

#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 796 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Sep 16, 2010
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.864→50 Å / Num. all: 97840 / Num. obs: 92657 / % possible obs: 94.6 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 1.2
Reflection shellResolution: 1.864→1.9 Å / % possible all: 92.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→38.25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.264 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20138 4852 5 %RANDOM
Rwork0.16959 ---
obs0.17118 92656 98.7 %-
all-97840 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.473 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0 Å20 Å2
2--0.9 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.86→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7343 620 37 796 8796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198320
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.90811399
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.185924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53924.127378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.903151358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8781548
X-RAY DIFFRACTIONr_chiral_restr0.090.21181
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216159
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.31544531
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3167358
X-RAY DIFFRACTIONr_scbond_it2.7863786
X-RAY DIFFRACTIONr_scangle_it4.20694017
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.912 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 280 -
Rwork0.269 5820 -
obs--87.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.38670.0753-0.08230.0431-0.01430.0273-0.1257-0.0516-0.1688-0.01690.0575-0.05470.01740.02280.06830.0620.02730.01990.1416-0.00160.162917.2292.821-35.439
20.20440.17520.10331.69610.56380.50050.01260.0024-0.05730.0784-0.04740.1040.0461-0.0810.03480.0099-0.01260.00970.0296-0.00530.0606-24.912-2.273-33.56
30.47680.2525-0.14180.7825-0.02861.16210.027-0.0625-0.03330.1069-0.06130.0037-0.06320.10130.03430.0191-0.00890.00170.03860.00870.008-10.5822.108-15.035
40.78760.48020.18480.92680.03810.3102-0.07480.2578-0.037-0.15970.1283-0.0398-0.00770.0791-0.05360.0346-0.02780.01190.0969-0.01970.01363.716.583-60.168
50.62450.2650.0383.1526-0.46810.4085-0.05650.07250.15150.05830.00580.0582-0.0898-0.03210.05070.02880.0023-0.01910.0440.01310.0445-9.38626.479-47.352
61.19540.17930.57210.7498-0.13491.0005-0.06820.04430.11820.01640.0430.0269-0.06510.01750.02520.0281-0.02460.00030.04310.00550.03039.42122.726-47.773
71.9092-0.0492-0.5360.6266-0.4222.1952-0.1346-0.39040.13070.0550.1613-0.0870.04110.2319-0.02670.01590.0469-0.02230.1478-0.06110.045822.15520.734-27.724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T1 - 18
2X-RAY DIFFRACTION1P103 - 114
3X-RAY DIFFRACTION1P115
4X-RAY DIFFRACTION1A1001
5X-RAY DIFFRACTION2A1 - 105
6X-RAY DIFFRACTION2A340 - 389
7X-RAY DIFFRACTION3A106 - 339
8X-RAY DIFFRACTION4A390 - 468
9X-RAY DIFFRACTION4A576 - 706
10X-RAY DIFFRACTION5A469 - 575
11X-RAY DIFFRACTION6A707 - 737
12X-RAY DIFFRACTION7A738 - 901

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