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- PDB-4fk4: RB69 DNA polymerase ternary complex with dGTP/dG -

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Basic information

Entry
Database: PDB / ID: 4fk4
TitleRB69 DNA polymerase ternary complex with dGTP/dG
Components
  • DNA polymerase
  • DNA primer
  • DNA template
KeywordsTransferase/DNA / dGTP/dG / RB69 / RB69 pol / quadruple / 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: 1.9 Å
AuthorsXia, S. / Wang, J. / Konigsberg, W.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase.
Authors: Xia, S. / Wang, J. / Konigsberg, W.H.
History
DepositionJun 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: 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)114,3459
Polymers113,6383
Non-polymers7086
Water11,223623
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-67 kcal/mol
Surface area42880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.799, 120.407, 130.727
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: 104448.867 Da / Num. of mol.: 1 / Mutation: D222A, D327A, L415A, 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 template


Mass: 5237.399 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, 629 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.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 52.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 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: 0.97 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: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 90886 / Num. obs: 86052 / % possible obs: 94.7 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 1.1
Reflection shellResolution: 1.9→1.97 Å / % possible all: 96.2

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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: 1.9→46.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.193 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22214 4538 5 %RANDOM
Rwork0.1879 ---
all0.1879 90886 --
obs0.18966 86052 94.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.251 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0 Å2
2---0.42 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7340 613 36 623 8612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228266
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1242.05911312
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2695908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.624.202376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.771151344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7321546
X-RAY DIFFRACTIONr_chiral_restr0.0750.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216118
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_it1.44344507
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.36867307
X-RAY DIFFRACTIONr_scbond_it2.89563759
X-RAY DIFFRACTIONr_scangle_it4.14594001
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.936 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 303 -
Rwork0.28 5623 -
obs--85.11 %
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)
10.23720.01870.07370.0530.01370.0261-0.12390.00810.1380.02290.06320.0575-0.02470.00460.06070.13830.0125-0.01570.12080.00930.173-17.181-2.806-35.774
20.05060.0667-0.10361.1942-0.41960.35990.0104-0.00360.03460.0582-0.0385-0.0933-0.02910.05440.02810.0834-0.0211-0.01130.05210.01480.114124.8172.158-33.647
30.37930.20990.11610.66220.00831.10570.0198-0.03640.0340.087-0.0546-0.00910.0676-0.07830.03480.0787-0.0067-0.0040.05-0.01010.043510.404-22.257-15.054
40.73330.5005-0.20330.9428-0.05440.2174-0.07330.24170.0339-0.14620.10620.0229-0.008-0.0738-0.03290.0979-0.0286-0.01580.11950.02410.0131-3.653-6.634-60.268
50.55340.023-0.04052.57590.4430.2433-0.05520.0947-0.1390.11780.0038-0.00040.0590.04450.05140.1022-0.00210.01360.0705-0.01980.06769.449-26.622-47.359
60.47990.424-0.0530.4955-0.15550.3264-0.05480.0554-0.0741-0.03670.07930.01210.02340.0122-0.02460.1101-0.02250.00620.0886-0.00650.0826-9.51-22.765-47.796
71.6005-0.14870.46210.44890.30821.5961-0.1113-0.306-0.12280.04750.1420.064-0.0508-0.1845-0.03070.08070.04360.03050.12090.05680.0779-22.334-20.893-27.911
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T2 - 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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