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- PDB-5oqq: Crystal structure of the S. cerevisiae condensin Ycg1-Brn1 subcomplex -

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Basic information

Entry
Database: PDB / ID: 5oqq
TitleCrystal structure of the S. cerevisiae condensin Ycg1-Brn1 subcomplex
Components
  • Condensin complex subunit 2
  • Condensin complex subunit 3
KeywordsCELL CYCLE / kleisin / HEAT repeat / DNA-binding / SMC complex
Function / homology
Function and homology information


negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / tRNA gene clustering / meiotic chromosome condensation / meiotic chromosome separation / condensin complex / rDNA chromatin condensation / synaptonemal complex assembly / mitotic chromosome condensation / chromosome condensation ...negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / tRNA gene clustering / meiotic chromosome condensation / meiotic chromosome separation / condensin complex / rDNA chromatin condensation / synaptonemal complex assembly / mitotic chromosome condensation / chromosome condensation / mitotic sister chromatid segregation / condensed chromosome / cell division / chromatin binding / nucleus / cytoplasm
Similarity search - Function
Nuclear condensin complex subunit 3, C-terminal domain / Condensin complex subunit 3 / Nuclear condensing complex subunits, C-term domain / Condensin complex subunit 2/barren / Condensin complex subunit 2 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Condensin complex subunit 2 / Condensin complex subunit 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsKschonsak, M. / Hassler, M. / Haering, C.H.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation5853/2 Germany
European Research CouncilERC-2015-CoG 681365
CitationJournal: Cell / Year: 2017
Title: Structural Basis for a Safety-Belt Mechanism That Anchors Condensin to Chromosomes.
Authors: Kschonsak, M. / Merkel, F. / Bisht, S. / Metz, J. / Rybin, V. / Hassler, M. / Haering, C.H.
History
DepositionAug 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Jan 17, 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

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Assembly

Deposited unit
A: Condensin complex subunit 3
B: Condensin complex subunit 3
D: Condensin complex subunit 2
C: Condensin complex subunit 2


Theoretical massNumber of molelcules
Total (without water)235,7014
Polymers235,7014
Non-polymers00
Water57632
1
A: Condensin complex subunit 3
C: Condensin complex subunit 2


Theoretical massNumber of molelcules
Total (without water)117,8512
Polymers117,8512
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-31 kcal/mol
Surface area41330 Å2
MethodPISA
2
B: Condensin complex subunit 3
D: Condensin complex subunit 2


Theoretical massNumber of molelcules
Total (without water)117,8512
Polymers117,8512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-36 kcal/mol
Surface area42630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.534, 185.534, 148.321
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Condensin complex subunit 3 / CAPG homolog


Mass: 99715.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: loop deletion: 499-555
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: YCG1, YCS5, YDR325W / Plasmid: pETMCN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: Q06680
#2: Protein Condensin complex subunit 2 / Barren homolog / CAPH homolog


Mass: 18134.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 384-529
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: BRN1, YBL097W, YBL0830 / Plasmid: pETMCN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: P38170
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 3% (w/v) PEG 4000, 0.1 M Na citrate pH 5.5 0.2 M Na acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→49.44 Å / Num. obs: 73424 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.046 / Net I/σ(I): 12.9
Reflection shellResolution: 2.79→2.94 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.745 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 10633 / CC1/2: 0.444 / Rpim(I) all: 0.564 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OQR

5oqr


Resolution: 2.79→47.254 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 1988 2.71 %
Rwork0.2047 --
obs0.2059 73424 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79→47.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14377 0 0 32 14409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314606
X-RAY DIFFRACTIONf_angle_d0.52719720
X-RAY DIFFRACTIONf_dihedral_angle_d17.1718972
X-RAY DIFFRACTIONf_chiral_restr0.0362299
X-RAY DIFFRACTIONf_plane_restr0.0032511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.85980.35341420.30635056X-RAY DIFFRACTION100
2.8598-2.93710.34251390.3075056X-RAY DIFFRACTION100
2.9371-3.02350.36211420.29295031X-RAY DIFFRACTION100
3.0235-3.12110.35321420.28555063X-RAY DIFFRACTION100
3.1211-3.23260.33571430.28185039X-RAY DIFFRACTION100
3.2326-3.3620.3091410.2465096X-RAY DIFFRACTION100
3.362-3.5150.26541440.22785068X-RAY DIFFRACTION100
3.515-3.70020.26021350.21575089X-RAY DIFFRACTION100
3.7002-3.93190.25381420.20355092X-RAY DIFFRACTION100
3.9319-4.23530.21281400.17765106X-RAY DIFFRACTION100
4.2353-4.66120.221450.16445125X-RAY DIFFRACTION100
4.6612-5.33490.20521430.17215110X-RAY DIFFRACTION100
5.3349-6.71840.24341460.2165171X-RAY DIFFRACTION100
6.7184-47.26070.21411440.1735334X-RAY DIFFRACTION100

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