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- PDB-3qex: RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dGTP... -

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Basic information

Entry
Database: PDB / ID: 3qex
TitleRB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dGTP Opposite dT
Components
  • DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3')
  • DNA (5'-D(*TP*CP*AP*TP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
  • DNA polymerase
KeywordsTransferase/DNA / Difluorotoluene Nucleoside / dGTP/dT / Triple mutant / 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'-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: 1.73 Å
AuthorsXia, S. / Konigsberg, W.H. / Wang, J.
CitationJournal: To be Published
Title: Hydrogen-Bonding Capability of Difluorotoluene Nucleoside in Replication Complexes
Authors: Xia, S. / Konigsberg, W.H. / Wang, J.
History
DepositionJan 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 21, 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 (5'-D(*TP*CP*AP*TP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
P: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6679
Polymers113,9593
Non-polymers7086
Water17,312961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-71 kcal/mol
Surface area42800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.991, 120.211, 130.361
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 / Plasmid: PSP72 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q38087, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA (5'-D(*TP*CP*AP*TP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')


Mass: 5516.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Template
#3: DNA chain DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3')


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

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Non-polymers , 3 types, 967 molecules

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


Mass: 18.015 Da / Num. of mol.: 961 / 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: 150 mM CaCl2, 15% (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-C / Wavelength: 0.97918 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Nov 15, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.73→30 Å / Num. all: 120208 / Num. obs: 113883 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 1.73→1.76 Å / % possible all: 78.7

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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: 1.73→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20627 6021 5 %RANDOM
Rwork0.17811 ---
obs0.17953 113883 97.06 %-
all-120208 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.156 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0 Å20 Å2
2--0.7 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.73→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7343 628 36 961 8968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228357
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1012.06111450
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0345928
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85324.219384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96151369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7681548
X-RAY DIFFRACTIONr_chiral_restr0.0730.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216200
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_it1.16144537
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0467368
X-RAY DIFFRACTIONr_scbond_it2.38363819
X-RAY DIFFRACTIONr_scangle_it3.64494068
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.774 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 347 -
Rwork0.332 6810 -
obs--79.2 %
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)
10.13670.01440.03520.0215-0.00260.0279-0.0817-0.01290.1043-0.01170.04090.02320.003-0.00910.04080.08570.0076-0.0270.11770.01580.1331-16.821-2.797-35.417
20.1350.1237-0.05160.9537-0.33890.2490.00240.01920.03210.0486-0.0221-0.0786-0.02220.04190.01960.0416-0.0149-0.01570.05260.01290.076325.0112.15-33.506
30.25450.22420.10580.52260.03830.67720.0228-0.02610.03550.0738-0.0554-0.0050.0485-0.05920.03250.0526-0.0081-0.01030.0632-0.00940.036910.6-22.12-15.1
40.63730.4229-0.21340.7686-0.03680.1252-0.05930.23860.0476-0.11220.09540.01690.0023-0.0862-0.03610.0628-0.0321-0.01620.13710.0240.0181-3.73-6.509-60.221
50.43780.1441-0.06532.0530.4050.2184-0.05210.099-0.09820.0915-0.0001-0.01980.0530.01810.05230.06650.00030.01040.0765-0.02250.04959.414-26.598-47.238
60.7482-0.0443-0.38350.38360.12230.339-0.04880.0368-0.10620.01450.0531-0.02120.0183-0.0119-0.00430.0658-0.02210.00120.0749-0.01930.0589-9.47-22.623-47.492
71.1567-0.07540.18980.33620.38231.1993-0.0749-0.212-0.10640.02360.10940.04810.003-0.0832-0.03450.03360.01770.01670.10570.05140.0456-22.093-20.763-27.677
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T1 - 18
2X-RAY DIFFRACTION1P103 - 115
3X-RAY DIFFRACTION1A904
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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