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- PDB-1g5i: CRYSTAL STRUCTURE OF THE ACCESSORY SUBUNIT OF MURINE MITOCHONDRIA... -

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Basic information

Entry
Database: PDB / ID: 1g5i
TitleCRYSTAL STRUCTURE OF THE ACCESSORY SUBUNIT OF MURINE MITOCHONDRIAL POLYMERASE GAMMA
ComponentsMITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
KeywordsDNA BINDING PROTEIN / intermolecular four helix bundle
Function / homology
Function and homology information


gamma DNA polymerase complex / mitochondrial DNA replication / mitochondrial DNA metabolic process / DNA polymerase processivity factor activity / mitochondrial nucleoid / DNA polymerase binding / mitochondrion organization / double-stranded DNA binding / DNA replication / in utero embryonic development ...gamma DNA polymerase complex / mitochondrial DNA replication / mitochondrial DNA metabolic process / DNA polymerase processivity factor activity / mitochondrial nucleoid / DNA polymerase binding / mitochondrion organization / double-stranded DNA binding / DNA replication / in utero embryonic development / DNA-directed DNA polymerase activity / mitochondrial matrix / DNA repair / mitochondrion / identical protein binding / cytoplasm
Similarity search - Function
Glycyl-tRNA synthetase-like core domain / 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) ...Glycyl-tRNA synthetase-like core domain / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsCarrodeguas, J.A. / Theis, K. / Bogenhagen, D.F. / Kisker, C.
Citation
Journal: Mol.Cell / Year: 2001
Title: Crystal structure and deletion analysis show that the accessory subunit of mammalian DNA polymerase gamma, Pol gamma B, functions as a homodimer.
Authors: Carrodeguas, J.A. / Theis, K. / Bogenhagen, D.F. / Kisker, C.
#1: Journal: Nucleic Acids Res. / Year: 2000
Title: Protein Sequences Conserved in Prokaryotic Aminoacyl-tRNA Synthetases are Important for the Activity of the Processivity Factor of Human Mitochondrial DNA Polymerase
Authors: Carrodeguas, J.A. / Bogenhagen, D.F.
History
DepositionNov 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
B: MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
C: MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
D: MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,49610
Polymers204,2204
Non-polymers2766
Water15,889882
1
A: MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
B: MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2485
Polymers102,1102
Non-polymers1383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-57 kcal/mol
Surface area34710 Å2
MethodPISA
2
C: MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
D: MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2485
Polymers102,1102
Non-polymers1383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-60 kcal/mol
Surface area35950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.743, 134.010, 135.144
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
MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT


Mass: 51054.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: DNA POLYMERASE GAMMA SUBUNIT B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QZM2
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
2300 mM1dropNaCl
320 mMHEPES1drop
40.5 Msodium citrate1reservoir
550 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.25→47.14 Å / Num. all: 81301 / Num. obs: 81301 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 39.853 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 21.5
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.96 / % possible all: 93
Reflection
*PLUS
% possible obs: 98 %
Reflection shell
*PLUS
% possible obs: 93 %

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Processing

Software
NameClassification
X-PLORrefinement
MARMADdata reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1G5H

1g5h


Resolution: 2.3→20 Å / SU B: 9.25 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -1000 / ESU R Free: 0.32
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1614 2 %RANDOM
Rwork0.189 ---
all0.189 79240 --
obs0.189 79240 96.5 %-
Displacement parametersBiso mean: 40.19 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12876 0 16 882 13774
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.35
X-RAY DIFFRACTIONx_mcbond_it2.779
X-RAY DIFFRACTIONx_mcangle_it4.313
X-RAY DIFFRACTIONx_scbond_it6.31
X-RAY DIFFRACTIONx_scangle_it8.909
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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