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

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Basic information

Entry
Database: PDB / ID: 3qev
TitleRB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dCTP 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*GP*TP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
  • DNA polymerase
KeywordsTransferase/DNA / Difluorotoluene Nucleoside / dCTP/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, palm domain / Palm domain of DNA polymerase / B family DNA polymerase, finger domain / DNA polymerase, palm domain superfamily ...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, palm domain / Palm domain of DNA polymerase / B family DNA polymerase, finger domain / DNA polymerase, palm domain superfamily / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / Monooxygenase / DNA polymerase family B, exonuclease domain / DNA polymerase family B / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, exonuclease domain / 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 (> 10) / DNA / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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

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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*GP*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)114,68310
Polymers113,9753
Non-polymers7087
Water16,250902
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-82 kcal/mol
Surface area42790 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)75.018, 119.553, 130.369
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 (bacteriophage)
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*GP*TP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')


Mass: 5532.577 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, 909 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.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 902 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
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: Oct 21, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 106517 / Num. obs: 100984 / % possible obs: 94.8 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 1.2
Reflection shellResolution: 1.77→1.81 Å / % possible all: 82.3

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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: 1.77→45.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20975 5308 5 %RANDOM
Rwork0.17309 ---
obs0.17492 100984 92.69 %-
all-106517 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.517 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å2-0 Å2
2---0.39 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.77→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7343 629 34 902 8908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228346
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0852.06111436
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0725928
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93524.162382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2151365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6741549
X-RAY DIFFRACTIONr_chiral_restr0.0720.21211
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216189
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_it1.16344537
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.04467369
X-RAY DIFFRACTIONr_scbond_it2.40563808
X-RAY DIFFRACTIONr_scangle_it3.66494053
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 327 -
Rwork0.326 6275 -
obs--78.85 %
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)
10.2346-0.00410.02440.02390.0090.0446-0.08660.02170.09920.01610.0434-0.02680.01420.02470.04320.1017-0.0085-0.02210.1622-0.00470.133716.755-2.83135.387
20.0955-0.122-0.05541.25340.41010.3861-0.00260.0130.0288-0.0497-0.02440.1082-0.0289-0.05580.02690.06040.0132-0.00480.0983-0.00340.0685-24.9722.29833.555
30.2889-0.18130.05570.5946-0.04590.85980.01290.0350.0187-0.0869-0.0466-0.00070.06680.06160.03360.07610.00670.00160.1030.00360.027-10.363-21.79415.108
40.5879-0.4245-0.10610.84070.04650.2558-0.0517-0.16530.01380.13920.0832-0.0112-0.00070.0629-0.03140.09520.0209-0.01490.1338-0.01140.01193.757-6.56660.159
50.3583-0.19130.03752.6929-0.33650.3209-0.029-0.0411-0.0912-0.06050.00260.03980.0754-0.01640.02630.0845-0.00060.01040.09380.00990.0412-9.32-26.72847.351
60.5206-0.29090.03120.35310.1910.2536-0.0342-0.0341-0.10190.01810.0280.04390.02950.01940.00610.10290.01960.00770.11380.01160.07199.611-22.49247.433
71.27510.11990.13730.5268-0.38341.2255-0.08660.2407-0.0803-0.0460.1053-0.05790.00120.0946-0.01880.0574-0.01640.01610.1309-0.04840.043922.201-20.54427.606
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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