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

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Basic information

Entry
Database: PDB / ID: 6cqo
TitleCrystal Structure of mitochondrial single-stranded DNA binding proteins from S. cerevisiae (SeMet Labeled), Rim1 (Form2)
ComponentsSingle-stranded DNA-binding protein RIM1, mitochondrial
KeywordsDNA BINDING PROTEIN / Mitochondrial single-stranded DNA binding proteins / Rim1 / S. cerevisiae
Function / homology
Function and homology information


positive regulation of mitochondrial DNA replication / mitochondrial DNA replication / mitochondrial genome maintenance / mitochondrial nucleoid / single-stranded DNA binding / 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 / SAD / 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 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 26, 2020Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rpim_I_all

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Single-stranded DNA-binding protein RIM1, mitochondrial
B: Single-stranded DNA-binding protein RIM1, mitochondrial
C: Single-stranded DNA-binding protein RIM1, mitochondrial
D: Single-stranded DNA-binding protein RIM1, mitochondrial
E: Single-stranded DNA-binding protein RIM1, mitochondrial
F: Single-stranded DNA-binding protein RIM1, mitochondrial
G: Single-stranded DNA-binding protein RIM1, mitochondrial
H: Single-stranded DNA-binding protein RIM1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)108,2378
Polymers108,2378
Non-polymers00
Water82946
1
A: Single-stranded DNA-binding protein RIM1, mitochondrial
G: Single-stranded DNA-binding protein RIM1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)27,0592
Polymers27,0592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-11 kcal/mol
Surface area10460 Å2
MethodPISA
2
B: Single-stranded DNA-binding protein RIM1, mitochondrial
F: Single-stranded DNA-binding protein RIM1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)27,0592
Polymers27,0592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-7 kcal/mol
Surface area10320 Å2
MethodPISA
3
C: Single-stranded DNA-binding protein RIM1, mitochondrial
D: Single-stranded DNA-binding protein RIM1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)27,0592
Polymers27,0592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-5 kcal/mol
Surface area11070 Å2
MethodPISA
4
E: Single-stranded DNA-binding protein RIM1, mitochondrial

H: Single-stranded DNA-binding protein RIM1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)27,0592
Polymers27,0592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_457x-1/2,-y+1/2,-z+21
Buried area2010 Å2
ΔGint-6 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.283, 101.576, 114.484
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
Single-stranded DNA-binding protein RIM1, mitochondrial / Mitochondrial ssDNA-binding protein


Mass: 13529.567 Da / Num. of mol.: 8 / Fragment: residues 17-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RIM1, YCR028C-A, YCR28C-A / Production host: Escherichia coli (E. coli) / References: UniProt: P32445
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
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: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→62.985 Å / Num. obs: 23661 / % possible obs: 99.9 % / Redundancy: 15.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.051 / Net I/σ(I): 16
Reflection shellResolution: 2.8→2.873 Å / Rmerge(I) obs: 1.23 / Num. measured obs: 15756 / Num. unique obs: 2302 / CC1/2: 0.732 / Rpim(I) all: 0.505

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→62.985 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 27.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 1195 5.05 %
Rwork0.2227 --
obs0.2254 23660 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→62.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6044 0 0 46 6090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026154
X-RAY DIFFRACTIONf_angle_d0.4178291
X-RAY DIFFRACTIONf_dihedral_angle_d12.2533656
X-RAY DIFFRACTIONf_chiral_restr0.042913
X-RAY DIFFRACTIONf_plane_restr0.0031059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.91210.34171180.29582450X-RAY DIFFRACTION100
2.9121-3.04460.31121240.26862457X-RAY DIFFRACTION100
3.0446-3.20520.31511560.26272426X-RAY DIFFRACTION100
3.2052-3.4060.2951240.23872480X-RAY DIFFRACTION100
3.406-3.66890.30311500.21722468X-RAY DIFFRACTION100
3.6689-4.03810.2761290.21022491X-RAY DIFFRACTION100
4.0381-4.62220.19491230.18232504X-RAY DIFFRACTION100
4.6222-5.82290.2571240.20022542X-RAY DIFFRACTION100
5.8229-63.00110.29621470.24112647X-RAY DIFFRACTION100

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