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- PDB-1g5h: CRYSTAL STRUCTURE OF THE ACCESSORY SUBUNIT OF MURINE MITOCHONDRIA... -

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Basic information

Entry
Database: PDB / ID: 1g5h
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 / MAD / Resolution: 1.95 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 1.3Oct 4, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)205,62110
Polymers205,3454
Non-polymers2766
Water15,709872
1
A: MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
B: MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,8115
Polymers102,6732
Non-polymers1383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-59 kcal/mol
Surface area34790 Å2
MethodPISA
2
C: MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
D: MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,8115
Polymers102,6732
Non-polymers1383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-60 kcal/mol
Surface area36020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.623, 133.422, 135.038
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: 51336.285 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.: 872 / 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: 2.12 Å3/Da / Density % sol: 41.94 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X251
SYNCHROTRONNSLS X26C21.1
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDJul 10, 2000
ADSC QUANTUM 42CCDJun 28, 2000
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 127289 / Num. obs: 127238 / % possible obs: 99.96 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 30.741 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 29.6
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / % possible all: 100
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
SHAKEmodel building
SnBphasing
SOLVEphasing
SHARPphasing
REFMACrefinement
MARMADdata reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.95→20 Å / SU B: 4.892 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -1000 / ESU R: 0.413 / ESU R Free: 0.21 / Stereochemistry target values: standard refmac5
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2545 2 %RANDOM
Rwork0.183 ---
obs0.183 124642 100 %-
all-124693 --
Displacement parametersBiso mean: 42.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12891 0 16 872 13779
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.021
X-RAY DIFFRACTIONp_mcbond_it4.7562
X-RAY DIFFRACTIONp_mcangle_it7.2343.5
X-RAY DIFFRACTIONp_scbond_it9.6445
X-RAY DIFFRACTIONp_scangle_it13.0768
X-RAY DIFFRACTIONp_angle_deg1.7141.951
X-RAY DIFFRACTIONp_plane_restr0.0080.02
X-RAY DIFFRACTIONp_chiral_restr0.110.2
X-RAY DIFFRACTIONp_singtor_nbd4.3413
X-RAY DIFFRACTIONp_multtor_nbd18.3215
Software
*PLUS
Name: REFMAC5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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