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- PDB-3ikl: Crystal structure of Pol gB delta-I4. -

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Basic information

Entry
Database: PDB / ID: 3ikl
TitleCrystal structure of Pol gB delta-I4.
ComponentsDNA polymerase subunit gamma-2, mitochondrial
KeywordsTRANSFERASE
Function / homology
Function and homology information


gamma DNA polymerase complex / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA polymerase processivity factor activity / mitochondrial nucleoid / DNA polymerase binding / Transcriptional activation of mitochondrial biogenesis / DNA-templated DNA replication / double-stranded DNA binding / in utero embryonic development ...gamma DNA polymerase complex / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA polymerase processivity factor activity / mitochondrial nucleoid / DNA polymerase binding / Transcriptional activation of mitochondrial biogenesis / DNA-templated DNA replication / double-stranded DNA binding / in utero embryonic development / DNA-directed DNA polymerase activity / mitochondrial matrix / mitochondrion / identical protein binding / cytoplasm
Similarity search - Function
POLG2, C-terminal / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold ...POLG2, C-terminal / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA polymerase subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLee, Y.S. / Kennedy, W.D. / Yin, Y.W.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Structural insight into processive human mitochondrial DNA synthesis and disease-related polymerase mutations.
Authors: Lee, Y.S. / Kennedy, W.D. / Yin, Y.W.
History
DepositionAug 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase subunit gamma-2, mitochondrial
B: DNA polymerase subunit gamma-2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)104,2332
Polymers104,2332
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-19 kcal/mol
Surface area33400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.430, 64.430, 260.704
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsA homodimeric protein

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Components

#1: Protein DNA polymerase subunit gamma-2, mitochondrial / Mitochondrial DNA polymerase accessory subunit / PolG-beta / MtPolB / DNA polymerase gamma ...Mitochondrial DNA polymerase accessory subunit / PolG-beta / MtPolB / DNA polymerase gamma accessory 55 kDa subunit / p55


Mass: 52116.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLG2, MTPOLB / References: UniProt: Q9UHN1, DNA-directed DNA polymerase

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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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.14 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 16573 / Observed criterion σ(F): 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-3000data reduction
HKL-3000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→45.82 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 50156.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.294 708 4.9 %RANDOM
Rwork0.257 ---
obs0.257 14327 74.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.5856 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 77.5 Å2
Baniso -1Baniso -2Baniso -3
1-16.74 Å20 Å20 Å2
2--16.74 Å20 Å2
3----33.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.58 Å
Luzzati d res low-5 Å
Luzzati sigma a0.93 Å0.82 Å
Refinement stepCycle: LAST / Resolution: 3.1→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5866 0 0 0 5866
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.067 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.466 49 4.6 %
Rwork0.386 1006 -
obs--33.1 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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