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- PDB-3o59: DNA polymerase D large subunit DP2(1-300) from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 3o59
TitleDNA polymerase D large subunit DP2(1-300) from Pyrococcus horikoshii
ComponentsDNA polymerase II large subunit
KeywordsTRANSFERASE / alpha helical structure / DNA POLYMERASE
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 / identical protein 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. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. ...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. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / 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 / HNH nuclease
Similarity search - Domain/homology
DNA polymerase II large subunit
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsYokoyama, H. / Shen, Y. / Matsui, I.
Citation
Journal: Febs Lett. / Year: 2011
Title: Novel structure of an N-terminal domain that is crucial for the dimeric assembly and DNA-binding of an archaeal DNA polymerase D large subunit from Pyrococcus horikoshii
Authors: Matsui, I. / Urushibata, Y. / Shen, Y. / Matsui, E. / Yokoyama, H.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Subunit interaction and regulation of activity through terminal domains of the family D DNA polymerase from Pyrococcus horikoshii
Authors: Shen, Y. / Tang, X.-F. / Matsui, I.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: DNA polymerase II large subunit


Theoretical massNumber of molelcules
Total (without water)33,9101
Polymers33,9101
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.042, 54.042, 173.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 33910.395 Da / Num. of mol.: 1 / Fragment: DP2 subunit, 1st part, Residues 1-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0121 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O57861, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO THE GENBANK NP_142130, THE FIRST THREE RESIDUES, M-V-L, ARE INCLUDED AS THE ORIGINAL ...ACCORDING TO THE GENBANK NP_142130, THE FIRST THREE RESIDUES, M-V-L, ARE INCLUDED AS THE ORIGINAL SEQUENCE. THE FRAGMENT INFROMATION IS ADJUSTED FOR IT.

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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: 1.87 Å3/Da / Density % sol: 34.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22.5% PEG 10000, 0.1M HEPES-NaOH, 40mM guanidine-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.9788, 0.9793, 0.9900
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 23, 2002 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.97931
30.991
ReflectionResolution: 2.2→50 Å / Num. obs: 13924 / % possible obs: 99 % / Redundancy: 27.3 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 77.9
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 14.4 / % possible all: 92.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→43.33 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.434 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27168 1362 9.9 %RANDOM
Rwork0.20626 ---
obs0.21246 12379 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 0 107 2016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221939
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.9842614
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1332485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85615365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4721516
X-RAY DIFFRACTIONr_chiral_restr0.1170.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211435
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_it0.9891.51206
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.80521940
X-RAY DIFFRACTIONr_scbond_it3.1273733
X-RAY DIFFRACTIONr_scangle_it5.0124.5674
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 98 -
Rwork0.265 831 -
obs--93.37 %

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