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- PDB-6cqk: Crystal Structure of mitochondrial single-stranded DNA binding pr... -

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Basic information

Entry
Database: PDB / ID: 6cqk
TitleCrystal Structure of mitochondrial single-stranded DNA binding proteins from S. cerevisiae, Rim1 (Form1)
ComponentsSsDNA-binding protein essential for mitochondrial genome maintenance
KeywordsDNA BINDING PROTEIN / Mitochondrial single-stranded DNA binding proteins / Rim1
Function / homology
Function and homology information


positive regulation of mitochondrial DNA replication / mitochondrial DNA replication / Mitochondrial protein degradation / mitochondrial nucleoid / enzyme activator activity / single-stranded DNA binding / DNA replication / mitochondrion
Similarity search - Function
Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / Single-stranded DNA-binding protein RIM1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSingh, S.P. / Kukshal, V. / Bona, P.D. / Lytle, A.K. / Edwin, A. / Galletto, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01GM098509 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: The mitochondrial single-stranded DNA binding protein from S. cerevisiae, Rim1, does not form stable homo-tetramers and binds DNA as a dimer of dimers.
Authors: Singh, S.P. / Kukshal, V. / De Bona, P. / Antony, E. / Galletto, R.
History
DepositionMar 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: SsDNA-binding protein essential for mitochondrial genome maintenance
B: SsDNA-binding protein essential for mitochondrial genome maintenance
C: SsDNA-binding protein essential for mitochondrial genome maintenance
D: SsDNA-binding protein essential for mitochondrial genome maintenance


Theoretical massNumber of molelcules
Total (without water)53,7434
Polymers53,7434
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-19 kcal/mol
Surface area18840 Å2
2
A: SsDNA-binding protein essential for mitochondrial genome maintenance
B: SsDNA-binding protein essential for mitochondrial genome maintenance


Theoretical massNumber of molelcules
Total (without water)26,8722
Polymers26,8722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-6 kcal/mol
Surface area10450 Å2
MethodPISA
3
C: SsDNA-binding protein essential for mitochondrial genome maintenance
D: SsDNA-binding protein essential for mitochondrial genome maintenance


Theoretical massNumber of molelcules
Total (without water)26,8722
Polymers26,8722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-7 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.500, 153.140, 118.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
SsDNA-binding protein essential for mitochondrial genome maintenance


Mass: 13435.777 Da / Num. of mol.: 4 / Fragment: residues 17-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RIM1, SCKG_5256, SCKG_5616 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A250WMX0, UniProt: P32445*PLUS

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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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 0.2 M MgCl2 and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97845 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jan 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 2.8→76.57 Å / Num. obs: 12631 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.05 / Net I/σ(I): 12
Reflection shellResolution: 2.8→2.873 Å / Rmerge(I) obs: 1.967 / Num. measured obs: 18326 / Num. unique obs: 1244 / CC1/2: 0.527 / Rpim(I) all: 0.527

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CQO

6cqo


Resolution: 2.8→76.57 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R: 1.866 / ESU R Free: 0.39 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27854 617 4.9 %RANDOM
Rwork0.24574 ---
obs0.24729 11992 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 77.62 Å2
Baniso -1Baniso -2Baniso -3
1-7.13 Å20 Å2-0 Å2
2---3.81 Å20 Å2
3----3.33 Å2
Refinement stepCycle: 1 / Resolution: 2.8→76.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 0 0 2896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022941
X-RAY DIFFRACTIONr_bond_other_d00.022677
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.9373966
X-RAY DIFFRACTIONr_angle_other_deg3.69436194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7055346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.48924.73148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.64115503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4451515
X-RAY DIFFRACTIONr_chiral_restr0.1040.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023211
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02608
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_it3.497.7081429
X-RAY DIFFRACTIONr_mcbond_other3.487.7081428
X-RAY DIFFRACTIONr_mcangle_it5.5811.5451760
X-RAY DIFFRACTIONr_mcangle_other5.58211.5461761
X-RAY DIFFRACTIONr_scbond_it3.7378.2321510
X-RAY DIFFRACTIONr_scbond_other3.7378.231508
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.11512.1762205
X-RAY DIFFRACTIONr_long_range_B_refined8.92785.0772967
X-RAY DIFFRACTIONr_long_range_B_other8.92685.0932968
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 47 -
Rwork0.448 876 -
obs--99.68 %

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