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- PDB-5oqr: Crystal structure of the S. pombe condensin Cnd3-Cnd2 subcomplex -

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Basic information

Entry
Database: PDB / ID: 5oqr
TitleCrystal structure of the S. pombe condensin Cnd3-Cnd2 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


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activator activity / Condensation of Prometaphase Chromosomes / CENP-A containing chromatin / DNA topoisomerase binding / condensin complex / rDNA heterochromatin / attachment of mitotic spindle microtubules to kinetochore / mitotic chromosome condensation / heterochromatin / condensed chromosome ...DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activator activity / Condensation of Prometaphase Chromosomes / CENP-A containing chromatin / DNA topoisomerase binding / condensin complex / rDNA heterochromatin / attachment of mitotic spindle microtubules to kinetochore / mitotic chromosome condensation / heterochromatin / condensed chromosome / cell division / DNA repair / chromatin binding / chromatin / nucleus / cytosol / 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 3 / Condensin complex subunit 2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Condensin complex subunit 3
B: Condensin complex subunit 3
C: Condensin complex subunit 2
D: Condensin complex subunit 2


Theoretical massNumber of molelcules
Total (without water)212,8414
Polymers212,8414
Non-polymers00
Water84747
1
A: Condensin complex subunit 3
C: Condensin complex subunit 2


Theoretical massNumber of molelcules
Total (without water)106,4202
Polymers106,4202
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-32 kcal/mol
Surface area38580 Å2
MethodPISA
2
B: Condensin complex subunit 3
D: Condensin complex subunit 2


Theoretical massNumber of molelcules
Total (without water)106,4202
Polymers106,4202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-37 kcal/mol
Surface area38140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.407, 142.113, 176.917
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 Condensin complex subunit 3 / / CAPG homolog / p100


Mass: 90813.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: loop deletion: 439-473
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: cnd3, SPCC188.03 / Plasmid: pETMCN / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): Rosetta (DE3) pLysS / References: UniProt: Q10429
#2: Protein Condensin complex subunit 2 / / Barren homolog / CAPH homolog / p105


Mass: 15606.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 416-544
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: cnd2, SPCC306.03c / Plasmid: pETMCN / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): Rosetta (DE3) pLysS / References: UniProt: Q9Y7R3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 280 K / Method: vapor diffusion
Details: 3 to 4% (w/v) PEG 4000, 0.1 M Na citrate pH 5.2 to 5.4, 0.2 M Na acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.61→49.06 Å / Num. obs: 68083 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.06 / Net I/σ(I): 11.2
Reflection shellResolution: 2.61→2.67 Å / Redundancy: 13 % / Rmerge(I) obs: 1.482 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4542 / CC1/2: 0.678 / Rpim(I) all: 0.425 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→49.059 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 1996 2.93 %
Rwork0.2228 --
obs0.2238 68083 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.61→49.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12985 0 0 47 13032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313187
X-RAY DIFFRACTIONf_angle_d0.56817800
X-RAY DIFFRACTIONf_dihedral_angle_d18.5758095
X-RAY DIFFRACTIONf_chiral_restr0.0352077
X-RAY DIFFRACTIONf_plane_restr0.0032253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.67530.38631400.33154570X-RAY DIFFRACTION98
2.6753-2.74760.35981420.3164640X-RAY DIFFRACTION99
2.7476-2.82840.29961380.30354588X-RAY DIFFRACTION99
2.8284-2.91970.31481390.29274640X-RAY DIFFRACTION99
2.9197-3.02410.3131420.29124699X-RAY DIFFRACTION100
3.0241-3.14510.35371420.29054688X-RAY DIFFRACTION100
3.1451-3.28820.28121420.26194714X-RAY DIFFRACTION100
3.2882-3.46150.31091410.2474670X-RAY DIFFRACTION100
3.4615-3.67840.27131430.22874730X-RAY DIFFRACTION100
3.6784-3.96230.26661430.20524728X-RAY DIFFRACTION100
3.9623-4.36080.23731430.18754772X-RAY DIFFRACTION100
4.3608-4.99120.20661430.17684778X-RAY DIFFRACTION100
4.9912-6.28640.22751470.21964841X-RAY DIFFRACTION100
6.2864-49.06790.20781510.18545029X-RAY DIFFRACTION100

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