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- PDB-4dtj: RB69 DNA Polymerase Ternary Complex with dTTP Opposite an Abasic ... -

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Basic information

Entry
Database: PDB / ID: 4dtj
TitleRB69 DNA Polymerase Ternary Complex with dTTP Opposite an Abasic Site and ddT/dA as the Penultimate Base-pair
Components
  • DNA polymerase
  • DNA primer
  • DNA template
KeywordsTransferase/DNA / abasic site / THF / RB69pol / dTTP / 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 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 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 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 RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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_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_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.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_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 template
P: DNA primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2869
Polymers113,6043
Non-polymers6836
Water16,322906
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-79 kcal/mol
Surface area42850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.150, 119.871, 130.538
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: 104228.688 Da / Num. of mol.: 1
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 template


Mass: 5392.481 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA primer


Mass: 3982.596 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 912 molecules

#4: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 906 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
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: Oct 15, 2011
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 92548 / Num. obs: 87843 / % possible obs: 94.9 % / Observed criterion σ(F): 8 / Observed criterion σ(I): 4
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.784 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20204 4643 5 %RANDOM
Rwork0.17154 ---
obs0.17308 87843 98.92 %-
all-92548 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7343 620 34 906 8903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0198328
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.90811405
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1415922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91624.151383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01151363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0591549
X-RAY DIFFRACTIONr_chiral_restr0.0820.21178
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216174
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 325 -
Rwork0.214 5944 -
obs--96.52 %
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)
10.4254-0.1141-0.05570.07090.02540.0205-0.088-0.0397-0.13150.01080.0569-0.008-0.00540.01920.03120.05550.01040.02380.0974-0.00420.143918.1872.663-34.85
20.02450.12390.03941.20.39040.31980.00250.0031-0.01930.0543-0.02430.06710.0063-0.04080.02180.0108-0.00920.0070.0331-0.00660.0642-25.118-2.357-33.65
30.220.2155-0.02430.5650.00310.81510.0125-0.0208-0.02450.0759-0.0379-0.0003-0.06140.0720.02550.021-0.00390.00060.04080.00660.0142-10.55922.042-14.884
40.47230.35120.12570.74010.020.2079-0.04310.1766-0.0235-0.10860.0722-0.01980.00260.0703-0.02910.0368-0.0230.01090.0949-0.01590.00853.5936.723-60.383
50.33490.15490.05352.4598-0.37920.1882-0.04330.06520.08340.07790.00130.0239-0.0423-0.01370.04210.0326-0.0031-0.00970.04560.01650.0306-9.5226.303-47.226
60.62090.18110.09130.31540.33920.3855-0.0210.04170.0925-0.00750.02730.0094-0.00550.0265-0.00640.0226-0.0251-0.00210.05180.01450.0329.30522.919-48.194
71.216-0.1368-0.27560.3946-0.31461.1362-0.0979-0.22430.09760.04010.118-0.06490.01550.0899-0.02010.01140.0294-0.01680.0854-0.04390.036422.37220.768-27.89
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T1 - 18
2X-RAY DIFFRACTION1P103 - 115
4X-RAY DIFFRACTION2A1 - 105
5X-RAY DIFFRACTION2A340 - 389
6X-RAY DIFFRACTION3A106 - 339
7X-RAY DIFFRACTION4A390 - 468
8X-RAY DIFFRACTION4A576 - 706
9X-RAY DIFFRACTION5A469 - 575
10X-RAY DIFFRACTION6A707 - 737
11X-RAY DIFFRACTION7A738 - 901

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