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- PDB-4m3r: RB69 DNA polymerase ternary complex with dT/dG at position n-1 of... -

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Basic information

Entry
Database: PDB / ID: 4m3r
TitleRB69 DNA polymerase ternary complex with dT/dG at position n-1 of primer/template duplex
Components
  • DNA polymerase
  • DNA primerPrimer (molecular biology)
  • DNA template
KeywordsHYDROLASE/DNA / RB69 pol / quadruple / dT/dG / n-1 / RB69 / HYDROLASE-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
ADENOSINE-5'-TRIPHOSPHATE / DNA (> 10) / DNA / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsXia, S. / Konigsberg, W.H.
CitationJournal: Protein Sci. / Year: 2014
Title: Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant.
Authors: Xia, S. / Konigsberg, W.H.
History
DepositionAug 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references

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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)114,14111
Polymers113,3543
Non-polymers7888
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-89 kcal/mol
Surface area42980 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)78.371, 119.391, 129.956
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 (bacteriophage)
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: 4938.215 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Oligo was synthesized at keck facilities. (Yale University)
#3: DNA chain DNA primer / Primer (molecular biology)


Mass: 3966.597 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Oligo was synthesized at keck facilities. (Yale University)

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Non-polymers , 3 types, 440 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 150 mM CaCl2, 12% (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: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2012
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. all: 74231 / Num. obs: 63924 / % possible obs: 86.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1.5
Reflection shellResolution: 2.07→2.15 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→47.53 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.176 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22085 3392 5 %RANDOM
Rwork0.17797 ---
obs0.18011 63924 90.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0 Å2
2---0.4 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.07→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7359 593 37 432 8421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0198250
X-RAY DIFFRACTIONr_bond_other_d0.0010.027466
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.89111281
X-RAY DIFFRACTIONr_angle_other_deg0.775317244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3215906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52324.149376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04151346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5161547
X-RAY DIFFRACTIONr_chiral_restr0.0640.21164
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218886
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021923
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.074→2.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 54 -
Rwork0.194 979 -
obs--18.9 %
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)
10.7444-0.0192-0.17620.2589-0.06290.0637-0.20480.0738-0.20290.00060.14410.05130.0409-0.0470.06070.0877-0.04170.01730.1433-0.00550.1502-18.5564.00736.424
20.2081-0.32540.22521.4466-0.50030.27340.06180.0082-0.0012-0.1111-0.0817-0.15380.06880.0360.01990.03510.02410.03410.06150.02950.108424.835-0.2332.168
30.3191-0.36970.19470.73610.17620.79010.04990.02130.0225-0.1728-0.0876-0.0642-0.0493-0.04440.03780.09520.02290.05550.05190.01810.04299.06523.81813.474
40.4348-0.26880.02670.59640.09860.323-0.0164-0.1726-0.03030.10070.0206-0.0230.0511-0.0748-0.00420.05790.0017-0.010.10810.02250.0096-2.3999.22760.448
50.1775-0.13580.02272.33820.73360.5256-0.0034-0.02730.0389-0.1918-0.0257-0.0897-0.12060.00380.02920.05210.0021-0.01480.0330.01150.05689.68928.55446.307
60.9185-0.08290.2320.79580.19170.1221-0.0249-0.136-0.01440.05190.02090.011-0.0054-0.05330.00410.0530.0187-0.01380.11260.00420.0257-9.30924.49547.973
70.9923-0.1649-0.6060.44460.38980.8864-0.01940.16720.027-0.0952-0.02360.0842-0.0605-0.25180.0430.05220.0198-0.040.1469-0.00720.0317-22.76821.61728.322
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T3 - 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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