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- PDB-5ijl: D-family DNA polymerase - DP2 subunit (catalytic subunit) -

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Basic information

Entry
Database: PDB / ID: 5ijl
TitleD-family DNA polymerase - DP2 subunit (catalytic subunit)
ComponentsDNA polymerase II large subunit
KeywordsTRANSFERASE / DNA polymerase D-family
Function / homology
Function and homology information


exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / intein-mediated protein splicing / DNA catabolic process / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
DNA polymerase II large subunit DP2 / DNA polymerase II large subunit DP2, N-terminal / DNA polymerase II large subunit DP2 / Intein splicing domain / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily
Similarity search - Domain/homology
DNA polymerase II large subunit
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å
AuthorsSauguet, L. / Raia, P. / De Larue, M.
CitationJournal: Nat Commun / Year: 2016
Title: Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography.
Authors: Sauguet, L. / Raia, P. / Henneke, G. / Delarue, M.
History
DepositionMar 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase II large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9103
Polymers120,7801
Non-polymers1312
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area40850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.820, 106.200, 110.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA polymerase II large subunit / / Pol II


Mass: 120779.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / Gene: polC, PYRAB01200, PAB2404 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V2F4, DNA-directed DNA polymerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 60mM MES pH 5.6, 300mM NaCl, 6% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.19→43.8 Å / Num. obs: 63302 / % possible obs: 99.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 49.98 Å2 / Net I/σ(I): 8.5
Reflection shellRsym value: 1.151

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.19→43.8 Å / Cor.coef. Fo:Fc: 0.9432 / Cor.coef. Fo:Fc free: 0.9278 / SU R Cruickshank DPI: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.212 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.18
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 3165 5 %RANDOM
Rwork0.199 ---
obs0.2008 63302 99.34 %-
Displacement parametersBiso mean: 53.38 Å2
Baniso -1Baniso -2Baniso -3
1--7.5119 Å20 Å20 Å2
2--3.9661 Å20 Å2
3---3.5458 Å2
Refine analyzeLuzzati coordinate error obs: 0.309 Å
Refinement stepCycle: LAST / Resolution: 2.19→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7525 0 2 242 7769
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017693HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0910407HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2709SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes189HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1095HARMONIC5
X-RAY DIFFRACTIONt_it7693HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion18.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion965SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance8HARMONIC1
X-RAY DIFFRACTIONt_utility_angle12HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8589SEMIHARMONIC4
LS refinement shellResolution: 2.19→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2752 216 5.01 %
Rwork0.2393 4094 -
all0.2411 4310 -
obs--92.84 %
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)
10.63590.02420.24670.7648-0.0191.158-0.039-0.0170.1125-0.00010.02160.0179-0.31210.06230.01740.01930.0069-0.0119-0.0853-0.0257-0.095461.823110.73714.6083
21.0380.4112-0.52910-0.48740.01540.03570.02510.0019-0.00520.0518-0.13810.0078-0.0037-0.0875-0.00730.04190.0055-0.0828-0.05120.00713.9991108.49524.909
30.9077-0.1673-0.46740.16910.04850.3831-0.00240.05020.00490.03430.00060.05230.008-0.08120.0019-0.0098-0.0074-0.0314-0.0786-0.0354-0.101114.051497.336419.8962
41.4631-0.1061-0.52860.7343-0.17841.355-0.0360.0498-0.0383-0.02460.0570.18670.0308-0.0126-0.021-0.03460.0059-0.0548-0.13270.0209-0.052651.000485.518414.2578
51.1449-0.3646-0.29110.0560.02200.01450.00140.07560.0015-0.00180.06750.08170.0174-0.0128-0.0129-0.02160.0265-0.0568-0.01540.036234.5737110.0320.3415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|4 - A|267 }
2X-RAY DIFFRACTION2{ A|268 - A|497 }
3X-RAY DIFFRACTION3{ A|498 - A|730 }
4X-RAY DIFFRACTION4{ A|731 - A|971 }
5X-RAY DIFFRACTION5{ A|972 - A|1034 }

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