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- PDB-4e3s: RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT -

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Basic information

Entry
Database: PDB / ID: 4e3s
TitleRB69 DNA Polymerase Ternary Complex with dQTP Opposite dT
Components
  • DNA polymerase
  • DNA primer
  • DNA template
KeywordsTransferase/DNA / dQTP / RB69pol / 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
Chem-QTP / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsXia, S. / Wang, J. / Konigsberg, W.H.
CitationJournal: Biochemistry / Year: 2012
Title: Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA.
Authors: Xia, S. / Christian, T.D. / Wang, J. / Konigsberg, W.H.
History
DepositionMar 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 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)114,3459
Polymers113,6553
Non-polymers6906
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-61 kcal/mol
Surface area43390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.166, 118.509, 130.667
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: 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: 5212.386 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, 510 molecules

#4: Chemical ChemComp-QTP / 3-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7-methyl-3H-imidazo[4,5-b]pyridine


Mass: 489.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N3O12P3
#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.: 504 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 150mM CaCl2, 15% PEG350 MME, 100mM sodium cacodylate (pH6.5), VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Oct 20, 2010
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 78654 / Num. obs: 74440 / % possible obs: 94.6 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 1.3
Reflection shellResolution: 2.04→2.08 Å / % possible all: 85.7

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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: 2.04→47.22 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.471 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21855 3951 5 %RANDOM
Rwork0.17987 ---
all0.1818 78654 --
obs0.1818 74440 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.725 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å2-0 Å20 Å2
2--1.75 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.04→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7362 611 35 504 8512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198264
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.91111299
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3615904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99324.187375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02151346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1681546
X-RAY DIFFRACTIONr_chiral_restr0.0810.21167
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216108
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: 2.04→2.085 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 258 -
Rwork0.264 4982 -
obs--96.48 %
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)
10.8787-0.09720.29930.1737-0.0570.1068-0.24550.18190.30690.02860.1318-0.1174-0.07490.03290.11370.0867-0.0578-0.04010.247-0.01280.24717.163-3.64336.367
20.1917-0.2238-0.14761.22120.40020.17610.03960.00580.0052-0.068-0.04140.076-0.0355-0.03760.00180.01510.0088-0.00870.08490.01450.1011-25.0980.16632.119
30.3233-0.2064-0.12160.5274-0.07730.30070.03810.0080.0269-0.1125-0.05470.0330.04150.01760.01660.05060.0148-0.02610.08390.00570.044-8.716-23.96413.464
40.3126-0.1677-0.03280.3708-0.16880.3127-0.0168-0.13970.0190.05760.02220.0184-0.0230.0556-0.00540.03480.00680.01070.1085-0.01440.03831.997-9.18660.63
50.3076-0.1996-0.05611.734-0.5240.2447-0.0343-0.0781-0.0716-0.08980.0210.08210.0471-0.00140.01330.02230.00020.01010.09440.01530.0773-9.874-28.71546.412
60.2056-0.0463-0.14150.28490.37910.5371-0.03680.0464-0.02140.02510.042-0.00610.04620.0322-0.00520.0290.01810.02030.11540.02390.07759.019-24.73948.234
71.5072-0.06730.40490.3942-0.34520.4822-0.07670.2735-0.0084-0.06130.031-0.06610.03790.1430.04570.0223-0.010.02570.1717-0.00430.040522.783-21.32828.529
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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