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- PDB-6xwx: Crystal structure of the Tof1-Csm3 complex -

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Basic information

Entry
Database: PDB / ID: 6xwx
TitleCrystal structure of the Tof1-Csm3 complex
Components
  • Chromosome segregation in meiosis protein
  • Uncharacterized protein,Uncharacterized protein
KeywordsREPLICATION / Fork Protection Complex / Replisome / Cohesion establishment / S phase checkpoint / Armadillo repeat
Function / homology
Function and homology information


: / DNA replication checkpoint signaling / negative regulation of DNA replication / meiotic cell cycle / cell cycle / DNA damage response / nucleus
Similarity search - Function
Chromosome segregation in meiosis protein 3 / TIPIN/Csm3/Swi3 / Replication Fork Protection Component Swi3 / Timeless, N-terminal / Timeless protein
Similarity search - Domain/homology
Chromosome segregation in meiosis protein / Topoisomerase 1-associated factor 1
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGrabarczyk, D.B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR5152/3-1 Germany
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Crystal structure and interactions of the Tof1-Csm3 (Timeless-Tipin) fork protection complex.
Authors: Grabarczyk, D.B.
History
DepositionJan 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: 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 / _citation_author.identifier_ORCID
Revision 1.2Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein,Uncharacterized protein
B: Chromosome segregation in meiosis protein
C: Uncharacterized protein,Uncharacterized protein
D: Chromosome segregation in meiosis protein
E: Uncharacterized protein,Uncharacterized protein
F: Chromosome segregation in meiosis protein


Theoretical massNumber of molelcules
Total (without water)247,3076
Polymers247,3076
Non-polymers00
Water0
1
A: Uncharacterized protein,Uncharacterized protein
B: Chromosome segregation in meiosis protein


Theoretical massNumber of molelcules
Total (without water)82,4362
Polymers82,4362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-25 kcal/mol
Surface area32230 Å2
MethodPISA
2
C: Uncharacterized protein,Uncharacterized protein
D: Chromosome segregation in meiosis protein


Theoretical massNumber of molelcules
Total (without water)82,4362
Polymers82,4362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-24 kcal/mol
Surface area32130 Å2
MethodPISA
3
E: Uncharacterized protein,Uncharacterized protein
F: Chromosome segregation in meiosis protein


Theoretical massNumber of molelcules
Total (without water)82,4362
Polymers82,4362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-18 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)264.472, 82.034, 161.165
Angle α, β, γ (deg.)90, 124.85, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein,Uncharacterized protein


Mass: 69540.414 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0029130 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S825
#2: Protein Chromosome segregation in meiosis protein /


Mass: 12895.146 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0011090 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S0S7

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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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium Acetate, 0.1 M Tris-HCl pH 7.5-8.5, 4-8% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.09→76.74 Å / Num. obs: 27164 / % possible obs: 89.8 % / Redundancy: 7 % / CC1/2: 0.996 / Rpim(I) all: 0.078 / Net I/σ(I): 7.1
Reflection shellResolution: 3.09→3.524 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1359 / CC1/2: 0.365 / Rpim(I) all: 0.737

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MQI

5mqi


Resolution: 3.1→45.73 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.741
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1353 -RANDOM
Rwork0.237 ---
obs0.238 27151 52.3 %-
Displacement parametersBiso mean: 123.41 Å2
Baniso -1Baniso -2Baniso -3
1--20.7353 Å20 Å22.6985 Å2
2--13.4256 Å20 Å2
3---7.3096 Å2
Refine analyzeLuzzati coordinate error obs: 0.64 Å
Refinement stepCycle: LAST / Resolution: 3.1→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15731 0 0 0 15731
LS refinement shellResolution: 3.1→3.39 Å
RfactorNum. reflection% reflection
Rfree0.2328 29 -
Rwork0.249 --
obs0.2482 544 4.51 %

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