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- PDB-4dtm: RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic ... -

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Basic information

Entry
Database: PDB / ID: 4dtm
TitleRB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddG/dC as the Penultimate Base-pair
Components
  • DNA polymerase
  • DNA primerPrimer (molecular biology)
  • DNA template
KeywordsTransferase/DNA / abasic site / THF / RB69pol / dCTP / 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 / 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)114,2729
Polymers113,6053
Non-polymers6686
Water12,611700
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-78 kcal/mol
Surface area42960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.178, 120.499, 130.752
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: 5368.457 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA primer / Primer (molecular biology)


Mass: 4007.609 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 706 molecules

#4: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#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 / Water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
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: 1.95→50 Å / Num. all: 86912 / Num. obs: 82442 / % possible obs: 94.9 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 1.3
Reflection shellResolution: 1.95→2.02 Å / % possible all: 99.9

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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: 1.95→45.65 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.014 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22007 4350 5 %RANDOM
Rwork0.18445 ---
obs0.18625 82442 99.36 %-
all-86912 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.784 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7343 620 33 700 8696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0198287
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.90811339
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0685910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49424.058377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.868151353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0531549
X-RAY DIFFRACTIONr_chiral_restr0.080.21172
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216125
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: 1.95→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 292 -
Rwork0.305 5550 -
obs--96.75 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.38070.08930.17120.04040.02350.1315-0.0926-0.0249-0.0467-0.02130.0338-0.0347-0.0382-0.02190.05870.0480.01160.01960.0846-0.01210.115417.3822.973-35.455
20.04180.11170.06920.9090.31350.19520.00250.0029-0.0170.0358-0.03450.05470-0.03920.0320.0381-0.00480.00470.0475-0.0150.0755-25.128-2.377-33.694
30.12520.1102-0.00770.46-0.12040.62460.0164-0.011-0.01910.0724-0.03110.0167-0.05640.05720.01470.053-0.00540.00820.04270.00150.0255-10.5822.121-14.954
40.45830.27060.16880.61950.05860.0984-0.03440.1905-0.0431-0.08470.0668-0.0145-0.00180.0686-0.03240.059-0.0250.01080.1096-0.01920.01443.5816.739-60.508
50.43720.1120.10491.6055-0.21310.0972-0.07750.10750.09320.08160.0418-0.0064-0.0292-0.01590.03570.062-0.008-0.00450.07890.02280.0363-9.53826.417-47.332
60.9885-0.23640.14430.1570.20920.73590.00840.09490.055-0.0071-0.00330.00630.03160.0585-0.00510.0463-0.0349-0.01010.06510.01060.04689.24823.021-48.333
71.1256-0.0464-0.25130.2518-0.42321.1596-0.0786-0.19390.10760.02020.0739-0.05540.00170.06210.00470.0210.0228-0.01560.0997-0.05310.041522.3720.959-28.007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T1 - 18
2X-RAY DIFFRACTION1P103 - 115
3X-RAY DIFFRACTION1A1001
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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